Proteomics

# Map Entrez IDs to gene symbols
PROT_entrez_to_symbol <- pluck(PROT_WGCNA, "modules") %>%
  dplyr::select(entrez_gene, gene_symbol) %>%
  distinct() %>%
  deframe()
head(PROT_entrez_to_symbol)
#>     26194     26195     26198     26196     26204     26199 
#>  "Mt-nd2"  "Mt-co1"  "Mt-co2" "Mt-atp8"  "Mt-co3"  "Mt-nd3"

# Genes by module
PROT_MOD_LIST <- pluck(PROT_WGCNA, "modules") %>%
  filter(moduleColor != "grey") %>%
  group_by(moduleID) %>%
  summarise(feature = list(unique(entrez_gene))) %>%
  deframe()
map(PROT_MOD_LIST, head)
#> $P1
#> [1]  26194  26196  26199  26201 362277 308900
#> 
#> $P2
#> [1] 292126 361458  60374 311551 360518 406230
#> 
#> $P3
#> [1] 406864 406163 287699 287700 309622 361710
#> 
#> $P4
#> [1] 365022 282844 295692 308576 361967 314313
#> 
#> $P5
#> [1] 315452 360548 363327 432360 406161 296654
#> 
#> $P6
#> [1] 406868 290783 293852 295490 299799 300046
#> 
#> $P7
#> [1] 300741 288923 295231 314246  24907 287432
#> 
#> $P8
#> [1] 288532 288652 291469 361977 287278 309452
#> 
#> $P9
#> [1]  26195  26198  26204  26192 315509 289217
#> 
#> $P10
#> [1] 444984 117526 192218 289504 300782 288718
#> 
#> $P11
#> [1] 408236 408247 296562 288416 304546 360504

# Number of unique genes in each module
lengths(PROT_MOD_LIST)
#>   P1   P2   P3   P4   P5   P6   P7   P8   P9  P10  P11 
#> 3860 1403 1391  728  667  434  414  233  227  191  159
#   P1   P2   P3   P4   P5   P6   P7   P8   P9  P10  P11
# 3860 1403 1391  728  667  434  414  233  227  191  159

# all genes
PROT_UNIVERSE <- unique(unlist(PROT_MOD_LIST))
head(PROT_UNIVERSE)
#> [1]  26194  26196  26199  26201 362277 308900

# Select gene sets that are largely unchanged when filtering
# to only those Entrez IDs present in the results.
PROT_MSIGDB <- MSIGDB_PATHWAYS %>%
  mutate(entrez_gene = map(entrez_gene, intersect, y = PROT_UNIVERSE),
         set_size_post = lengths(entrez_gene),
         ratio = set_size_post / set_size) %>%
  filter(ratio >= 0.85, # at least 85% of the original set remains
         set_size_post >= 15)
head(PROT_MSIGDB)
#>   gs_subcat gs_exact_source
#> 1     GO:BP      GO:0006103
#> 2     GO:BP      GO:0006085
#> 3     GO:BP      GO:0006084
#> 4     GO:BP      GO:0043038
#> 5     GO:BP      GO:0046033
#> 6     GO:BP      GO:0019884
#>                                             gs_description  entrez_gene
#> 1                         2-oxoglutarate metabolic process 29416, 3....
#> 2                          acetyl-CoA biosynthetic process 25014, 2....
#> 3                             acetyl-CoA metabolic process 29416, 2....
#> 4                                    Amino acid activation 292023, ....
#> 5                                    AMP metabolic process 24165, 2....
#> 6 Antigen processing and presentation of exogenous antigen 309969, ....
#>   set_size set_size_post     ratio
#> 1       17            16 0.9411765
#> 2       17            17 1.0000000
#> 3       32            29 0.9062500
#> 4       45            42 0.9333333
#> 5       25            24 0.9600000
#> 6       35            30 0.8571429

# How many sets in each category remain?
table(PROT_MSIGDB$gs_subcat)
#> 
#> GO:BP GO:CC GO:MF 
#>   230    97    77
# GO:BP GO:CC GO:MF
#   230    97    77
# ORA
PROT_MODULE_ORA <- fora2(pathways = PROT_MSIGDB,
                         genes = PROT_MOD_LIST,
                         universe = PROT_UNIVERSE,
                         adjust.method = "scale",
                         adjust.globally = TRUE) %>%
  mutate(overlapGenes_symbol = map(
    .x = overlapGenes,
    .f = ~ na.omit(PROT_entrez_to_symbol[as.character(.x)])
  )) %>%
  relocate(module, gs_subcat, pathway, gs_description) %>%
  relocate(overlap, maxOverlap, overlapRatio, .after = size)

head(PROT_MODULE_ORA)
#>    module gs_subcat    pathway                               gs_description
#>    <fctr>    <char>     <char>                                       <char>
#> 1:     P1     GO:CC GO:0098798     Mitochondrial protein-containing complex
#> 2:     P1     GO:CC GO:0098800 Inner mitochondrial membrane protein complex
#> 3:     P1     GO:CC GO:0005840                                     Ribosome
#> 4:     P1     GO:MF GO:0003735           Structural constituent of ribosome
#> 5:     P1     GO:BP GO:0006119                    Oxidative phosphorylation
#> 6:     P1     GO:CC GO:0044391                            Ribosomal subunit
#>            pval         padj  size overlap maxOverlap overlapRatio overlapGenes
#>           <num>        <num> <int>   <int>      <int>        <num>       <list>
#> 1: 1.301385e-16 1.624359e-16   247     164        164    0.9939394 307350, ....
#> 2: 2.749959e-17 9.188149e-11   130     100        164    0.6060606 307350, ....
#> 3: 2.123303e-12 2.753016e-09   183     121        164    0.7333333 192210, ....
#> 4: 3.701938e-14 4.975619e-09   142     102        164    0.6181818 691075, ....
#> 5: 5.900244e-16 7.547399e-09   113      88        164    0.5333333 363516, ....
#> 6: 2.228687e-12 2.778986e-08   157     107        164    0.6484848 502531, ....
#>    overlapGenes_symbol
#>                 <list>
#> 1:        Afg3l2, ....
#> 2:        Afg3l2, ....
#> 3:        Dnajc21,....
#> 4:        Mrpl10, ....
#> 5:        Abcd1, A....
#> 6:        Eif2a, F....

Transcriptomics

TRNSCRPT_MODULES <- pluck(TRNSCRPT_WGCNA, "modules") %>%
  separate_rows(entrez_gene, gene_symbol, sep = ";") %>%
  filter(entrez_gene != "NA",
         moduleColor != "grey")
head(TRNSCRPT_MODULES)
#> # A tibble: 6 × 5
#>   moduleColor moduleID feature_ID         gene_symbol entrez_gene
#>   <chr>       <fct>    <chr>              <chr>       <chr>      
#> 1 turquoise   T1       ENSRNOG00000000007 Gad1        24379      
#> 2 blue        T2       ENSRNOG00000000008 Alx4        296511     
#> 3 yellow      T4       ENSRNOG00000000010 Cbln1       498922     
#> 4 green       T5       ENSRNOG00000000012 Tcf15       296272     
#> 5 turquoise   T1       ENSRNOG00000000017 Steap1      297738     
#> 6 green       T5       ENSRNOG00000000024 Hebp1       362454

# Entrez to gene symbol conversion vector
TRNSCRPT_entrez_to_symbol <- TRNSCRPT_MODULES %>%
  dplyr::select(entrez_gene, gene_symbol) %>%
  distinct() %>%
  deframe()
head(TRNSCRPT_entrez_to_symbol)
#>    24379   296511   498922   296272   297738   362454 
#>   "Gad1"   "Alx4"  "Cbln1"  "Tcf15" "Steap1"  "Hebp1"

# Genes by module
TRNSCRPT_MOD_LIST <- TRNSCRPT_MODULES %>%
  group_by(moduleID) %>%
  summarise(feature = list(unique(entrez_gene))) %>%
  deframe()
map(TRNSCRPT_MOD_LIST, head)
#> $T1
#> [1] "24379"  "297738" "305095" "83628"  "81659"  "64832" 
#> 
#> $T2
#> [1] "296511" "64076"  "360904" "306338" "85435"  "502585"
#> 
#> $T3
#> [1] "25419"  "305633" "290923" "81660"  "691729" "287561"
#> 
#> $T4
#> [1] "498922" "305101" "289424" "295568" "313806" "291359"
#> 
#> $T5
#> [1] "296272" "362454" "312754" "289883" "24184"  "81718" 
#> 
#> $T6
#> [1] "317628" "309626" "81773"  "81729"  "361856" "83474" 
#> 
#> $T7
#> [1] "140608" "362607" "301111" "294320" "294362" "288615"
#> 
#> $T8
#> [1] "362841" "29513"  "304555" "171387" "252860" "689074"
#> 
#> $T9
#> [1] "309760" "309772" "499430" "364147" "117052" "302920"
#> 
#> $T10
#> [1] "365542" "690865" "24699"  "361795" "25008"  "171075"
#> 
#> $T11
#> [1] "100365935" "309659"    "361831"    "25177"     "29353"     "304469"   
#> 
#> $T12
#> [1] "361811" "81917"  "360811" "360466" "287773" "317343"
#> 
#> $T13
#> [1] "360731" "246334" "305307" "287701" "296188" "305078"
#> 
#> $T14
#> [1] "360800" "81829"  "363790" "25405"  "299104" "287644"

# Number of unique genes in each module
lengths(TRNSCRPT_MOD_LIST)
#>   T1   T2   T3   T4   T5   T6   T7   T8   T9  T10  T11  T12  T13  T14 
#> 4425 3061 2014 1435  528  418  314  221  202  153  112   97   49   32
#   T1   T2   T3   T4   T5   T6   T7   T8   T9  T10  T11  T12  T13  T14
# 4425 3061 2014 1435  528  418  314  221  202  153  112   97   49   32

# all genes
TRNSCRPT_UNIVERSE <- unique(unlist(TRNSCRPT_MOD_LIST))
head(TRNSCRPT_UNIVERSE)
#> [1] "24379"  "297738" "305095" "83628"  "81659"  "64832"

# Select gene sets that are largely unchanged when filtering
# to only those Entrez IDs present in the results.
TRNSCRPT_MSIGDB <- MSIGDB_PATHWAYS %>%
  mutate(entrez_gene = map(entrez_gene, intersect, y = TRNSCRPT_UNIVERSE),
         set_size_post = lengths(entrez_gene),
         ratio = set_size_post / set_size) %>%
  filter(ratio >= 0.85, # at least 85% of the original set remains
         set_size_post >= 15)

# How many sets in each category remain?
table(TRNSCRPT_MSIGDB$gs_subcat)
#> 
#> GO:BP GO:CC GO:MF 
#>   927   110   158
# GO:BP GO:CC GO:MF
#   927   110   158
# ORA
TRNSCRPT_MODULE_ORA <- fora2(pathways = TRNSCRPT_MSIGDB,
                             genes = TRNSCRPT_MOD_LIST,
                             universe = TRNSCRPT_UNIVERSE,
                             adjust.method = "scale",
                             adjust.globally = TRUE) %>%
  mutate(overlapGenes_symbol = map(
    .x = overlapGenes,
    .f = ~ na.omit(TRNSCRPT_entrez_to_symbol[as.character(.x)])
  )) %>%
  relocate(module, gs_subcat, pathway, gs_description) %>%
  relocate(overlap, maxOverlap, overlapRatio, .after = size)

head(TRNSCRPT_MODULE_ORA)
#>    module gs_subcat    pathway
#>    <fctr>    <char>     <char>
#> 1:     T1     GO:BP GO:0048193
#> 2:     T1     GO:CC GO:0098798
#> 3:     T1     GO:CC GO:0000313
#> 4:     T1     GO:BP GO:0006888
#> 5:     T1     GO:CC GO:0140534
#> 6:     T1     GO:BP GO:0007030
#>                                               gs_description         pval
#>                                                       <char>        <num>
#> 1:                                   Golgi vesicle transport 1.312359e-18
#> 2:                  Mitochondrial protein-containing complex 7.043475e-15
#> 3:                                       Organellar ribosome 2.924571e-27
#> 4: Endoplasmic reticulum to Golgi vesicle-mediated transport 1.001808e-19
#> 5:          Endoplasmic reticulum protein-containing complex 2.318285e-17
#> 6:                                        Golgi organization 1.024182e-12
#>            padj  size overlap maxOverlap overlapRatio overlapGenes
#>           <num> <int>   <int>      <int>        <num>       <list>
#> 1: 1.708758e-18   255     155        155    0.9935897 114024, ....
#> 2: 1.616504e-13   242     141        155    0.9038462 307350, ....
#> 3: 1.240926e-12    75      70        155    0.4487179 290645, ....
#> 4: 5.883736e-11   110      84        155    0.5384615 300674, ....
#> 5: 1.803222e-09   112      82        155    0.5256410 362031, ....
#> 6: 8.478755e-07   120      79        155    0.5064103 246150, ....
#>    overlapGenes_symbol
#>                 <list>
#> 1:        Acsl3, A....
#> 2:        Afg3l2, ....
#> 3:        Mpv17l2,....
#> 4:        Arcn1, A....
#> 5:        Alg14, A....
#> 6:        Akap9, A....

Metabolomics

# List of features by module
METAB_MOD_LIST <- pluck(METAB_WGCNA, "modules") %>%
  filter(moduleColor != "grey") %>%
  group_by(moduleID) %>%
  summarise(feature = list(unique(feature_ID))) %>%
  deframe()
head(METAB_MOD_LIST)
#> $M1
#>   [1] "adenosine"                                                                                                
#>   [2] "Anserine"                                                                                                 
#>   [3] "C12 carnitine"                                                                                            
#>   [4] "C12:1 carnitine"                                                                                          
#>   [5] "C14 carnitine"                                                                                            
#>   [6] "C14:1 carnitine"                                                                                          
#>   [7] "C14:2 carnitine"                                                                                          
#>   [8] "C18:1 carnitine"                                                                                          
#>   [9] "C18:2 carnitine"                                                                                          
#>  [10] "C2 carnitine"                                                                                             
#>  [11] "C20 carnitine"                                                                                            
#>  [12] "C3 carnitine"                                                                                             
#>  [13] "Carnosine"                                                                                                
#>  [14] "Cer(d34:1)>Cer(d18:1/16:0)_feature1"                                                                      
#>  [15] "choline"                                                                                                  
#>  [16] "creatine"                                                                                                 
#>  [17] "deoxycholate"                                                                                             
#>  [18] "C34:1 DAG"                                                                                                
#>  [19] "gamma-glutamylleucine"                                                                                    
#>  [20] "glutathione reduced"                                                                                      
#>  [21] "inosine"                                                                                                  
#>  [22] "kynurenate"                                                                                               
#>  [23] "LPC(20:3)_a_b"                                                                                            
#>  [24] "N-acetylleucine"                                                                                          
#>  [25] "PC(30:0)"                                                                                                 
#>  [26] "PC(32:2)"                                                                                                 
#>  [27] "PC(36:2)"                                                                                                 
#>  [28] "SM(d34:0)_feature1"                                                                                       
#>  [29] "SM(d34:2)_feature1"                                                                                       
#>  [30] "sphinganine"                                                                                              
#>  [31] "sphingosine-1P (C18)"                                                                                     
#>  [32] "urocanate"                                                                                                
#>  [33] "xanthine"                                                                                                 
#>  [34] "alpha-Amino-N-butyric-acid"                                                                               
#>  [35] "CoA(10:2)"                                                                                                
#>  [36] "CoA(12:0-OH)"                                                                                             
#>  [37] "CoA(12:3)"                                                                                                
#>  [38] "CoA(16:0)"                                                                                                
#>  [39] "CoA(16:1)"                                                                                                
#>  [40] "CoA(19:3)"                                                                                                
#>  [41] "CoA(21:3)"                                                                                                
#>  [42] "CoA(9:1)"                                                                                                 
#>  [43] "NaMN"                                                                                                     
#>  [44] "ZMP"                                                                                                      
#>  [45] "dTTP"                                                                                                     
#>  [46] "13-HpODE"                                                                                                 
#>  [47] "9-HOTrE"                                                                                                  
#>  [48] "LTB4"                                                                                                     
#>  [49] "3-(1-pyrazolyl)-alanine_feature1"                                                                         
#>  [50] "Car(18:2)_feature1"                                                                                       
#>  [51] "Cer(d36:2)>Cer(d18:2/18:0)_feature1"                                                                      
#>  [52] "Cer(d40:1)>Cer(d18:1/22:0)_feature2"                                                                      
#>  [53] "Cer(d41:1)>Cer(d18:1/23:0)_feature1"                                                                      
#>  [54] "Cer(d42:1)>Cer(d18:1/24:0)_feature3"                                                                      
#>  [55] "Cer(d44:2)>Cer(d18:1/26:1)_feature2"                                                                      
#>  [56] "LPC(20:1/0:0)_and_LPC(0:0/20:1)_feature3"                                                                 
#>  [57] "PC(30:0)_feature1"                                                                                        
#>  [58] "PC(34:4)_feature2"                                                                                        
#>  [59] "PC(35:2)_feature2"                                                                                        
#>  [60] "PC(35:3)_feature1"                                                                                        
#>  [61] "PC(35:3)_feature3"                                                                                        
#>  [62] "PC(36:0)_feature3"                                                                                        
#>  [63] "PC(36:1)_feature1"                                                                                        
#>  [64] "PC(36:2)_feature3"                                                                                        
#>  [65] "PC(36:4)_feature3"                                                                                        
#>  [66] "PC(36:5)_feature1"                                                                                        
#>  [67] "PC(36:5)_feature2"                                                                                        
#>  [68] "PC(37:3)_feature2"                                                                                        
#>  [69] "PC(37:6)_feature4"                                                                                        
#>  [70] "PC(42:6)_feature2"                                                                                        
#>  [71] "PC(O-36:2)_feature3"                                                                                      
#>  [72] "PC(O-38:6)_feature1"                                                                                      
#>  [73] "PE(34:2)_feature2"                                                                                        
#>  [74] "PE(36:5)_feature5"                                                                                        
#>  [75] "PE(38:5)>PE(18:1_20:4)_feature7"                                                                          
#>  [76] "PE(38:5)>PE(18:1_20:4)_feature8"                                                                          
#>  [77] "PE(O-40:7)>PE(O-18:2/22:5)_feature4"                                                                      
#>  [78] "PS(40:4)_feature1"                                                                                        
#>  [79] "PS(40:6)_feature2"                                                                                        
#>  [80] "SM(d36:0)_feature1"                                                                                       
#>  [81] "SM(d38:1)_feature2"                                                                                       
#>  [82] "SM(d39:1)_feature2"                                                                                       
#>  [83] "SM(d41:1)_feature1"                                                                                       
#>  [84] "SM(d44:2)_feature1"                                                                                       
#>  [85] "TG(36:1)>TG(8:0_10:0_18:1)_and_TG(10:0_10:0_16:1)_feature3"                                               
#>  [86] "TG(36:2)_M+NH3_feature2"                                                                                  
#>  [87] "TG(38:2)>TG(4:0_16:1_18:1)_and_TG(4:0_16:0_18:2)_M+NH3_feature1"                                          
#>  [88] "TG(38:2)>TG(4:0_16:1_18:1)_and_TG(4:0_16:0_18:2)_feature3"                                                
#>  [89] "TG(39:1)_M+NH3_feature1"                                                                                  
#>  [90] "TG(40:4)>TG(4:0_18:2_18:2)_M+NH3_feature1"                                                                
#>  [91] "TG(40:5)>TG(4:0_18:2_18:3)_M+NH3_feature1"                                                                
#>  [92] "TG(41:3)>TG(5:0_18:1_18:2)_M+NH3_feature1"                                                                
#>  [93] "TG(42:1)_feature1"                                                                                        
#>  [94] "TG(42:2)_M+NH3_feature2"                                                                                  
#>  [95] "TG(42:3)>TG(6:0_18:1_18:2)_feature2"                                                                      
#>  [96] "TG(42:3)_M+NH3_feature1"                                                                                  
#>  [97] "TG(42:5)_M+NH3_feature1"                                                                                  
#>  [98] "TG(42:5)_M+NH3_feature2"                                                                                  
#>  [99] "TG(43:2)>TG(10:0_15:0_18:2)_M+NH3_feature1"                                                               
#> [100] "TG(44:1)>TG(10:0_16:0_18:1)_M+NH3_feature1"                                                               
#> [101] "TG(44:1)>TG(10:0_16:0_18:1)_feature3"                                                                     
#> [102] "TG(44:2)>TG(10:0_16:1_18:1)_M+NH3_feature1"                                                               
#> [103] "TG(44:2)>TG(10:0_16:1_18:1)_feature2"                                                                     
#> [104] "TG(44:3)>TG(8:0_18:1_18:2)_and_TG(10:0_16:1_18:2)_feature1"                                               
#> [105] "TG(44:4)>TG(8:0_18:2_18:2)_feature1"                                                                      
#> [106] "TG(45:2)_M+NH3_feature1"                                                                                  
#> [107] "TG(45:3)>TG(10:0_17:1_18:2)_and_TG(9:0_18:1_18:2)_M+NH3_feature1"                                         
#> [108] "TG(46:3)>TG(10:0_18:1_18:2)_and_TG(12:0_16:1_18:2)_feature1"                                              
#> [109] "TG(46:4)>TG(10:0_18:2_18:2)_feature1"                                                                     
#> [110] "TG(46:5)>TG(10:0_18:2_18:3)_feature1"                                                                     
#> [111] "TG(46:5)>TG(10:0_18:2_18:3)_feature2"                                                                     
#> [112] "TG(46:6)>TG(8:0_16:0_22:6)_M+NH3_feature1"                                                                
#> [113] "TG(46:6)>TG(8:0_18:2_20:4)_M+NH3_feature2"                                                                
#> [114] "TG(47:3)_M+NH3_feature2"                                                                                  
#> [115] "TG(48:1)>TG(16:0_16:0_16:1)_and_TG(14:0_16:0_18:1)_feature3"                                              
#> [116] "TG(48:2)>TG(14:0_16:0_18:2)_and_TG(14:0_16:1_18:1)_M+NH3_feature2"                                        
#> [117] "TG(48:2)>TG(14:0_16:0_18:2)_and_TG(14:0_16:1_18:1)_feature3"                                              
#> [118] "TG(48:3)_M+NH3_feature1"                                                                                  
#> [119] "TG(48:5)_feature1"                                                                                        
#> [120] "TG(48:6)>TG(10:0_16:0_22:6)_M+NH3_feature2"                                                               
#> [121] "TG(48:6)>TG(10:0_18:2_20:4)_M+NH3_feature1"                                                               
#> [122] "TG(49:0)>TG(16:0_16:0_17:0)_and_TG(15:0_16:0_18:0)_and_TG(14:0_16:0_19:0)_M+NH3_feature1"                 
#> [123] "TG(49:1)>TG(15:0_16:0_18:0)_and_TG(16:0_16:0_17:1)_and_>TG(16:0_16:1_17:0)_M+NH3_feature1"                
#> [124] "TG(49:2)_M+NH3_feature3"                                                                                  
#> [125] "TG(49:3)_M+NH3_feature1"                                                                                  
#> [126] "TG(49:3)_feature2"                                                                                        
#> [127] "TG(49:4)_M+NH3_feature1"                                                                                  
#> [128] "TG(50:1)>TG(16:0_16:0_18:1)_feature4"                                                                     
#> [129] "TG(50:1)_M+NH3_feature2"                                                                                  
#> [130] "TG(50:2)>TG(16:0_16:0_18:2)_and_TG(16:0_16:1_18:1)_M+NH3_feature1"                                        
#> [131] "TG(50:2)>TG(16:0_16:0_18:2)_and_TG(16:0_16:1_18:1)_M+NH3_feature2"                                        
#> [132] "TG(50:2)>TG(16:0_16:0_18:2)_and_TG(16:0_16:1_18:1)_M+NH3_feature3"                                        
#> [133] "TG(50:3)_M+NH3_feature4"                                                                                  
#> [134] "TG(50:3)_feature3"                                                                                        
#> [135] "TG(50:4)>TG(16:1_16:1_18:2)_feature2"                                                                     
#> [136] "TG(50:5)_M+NH3_feature1"                                                                                  
#> [137] "TG(50:5)_feature2"                                                                                        
#> [138] "TG(50:6)_feature2"                                                                                        
#> [139] "TG(50:7)>TG(10:0_18:2_22:5)_M+NH3_feature1"                                                               
#> [140] "TG(50:8)>TG(10:0_18:2_22:6)_and_TG(50:8)>TG(10:0_20:4_20:4)_M+NH3_feature1"                               
#> [141] "TG(51:0)>TG(16:0_17:0_18:0)_and_TG(16:0_16:0_19:0)_and_TG(15:0_17:0_19:0)_M+NH3_feature1"                 
#> [142] "TG(51:2)>TG(15:0_18:1_18:1)_and_TG(16:0_17:1_18:1)_and_TG(16:1_17:0_18:1)_M+NH3_feature2"                 
#> [143] "TG(51:3)>TG(15:0_18:1_18:2)_and_TG(16:0_17:1_18:2)_and_TG(16:1_17:1_18:1)_feature3"                       
#> [144] "TG(51:4)>TG(16:1_17:1_18:2)_and_TG(15:0_18:2_18:2)_and_TG(15:1_18:1_18:2)_feature1"                       
#> [145] "TG(51:5)>TG(15:0_18:2_18:3)_and_TG(15:1_18:2_18:2)_M+NH3_feature2"                                        
#> [146] "TG(52:1)_M+NH3_feature3"                                                                                  
#> [147] "TG(52:2)>TG(16:0_18:1_18:1)_and_TG(16:0_18:0_18:2)_M+NH3_feature5"                                        
#> [148] "TG(52:2)>TG(16:0_18:1_18:1)_and_TG(16:0_18:0_18:2)_M+NH3_feature7"                                        
#> [149] "TG(52:3)>TG(16:0_18:1_18:2)_and_TG(16:1_18:1_18:1)_feature3"                                              
#> [150] "TG(52:4)>TG(16:0_16:0_20:4)_and_TG(16:1_18:1_18:2)_and_TG(16:0_18:1_18:2)_M+NH3_feature6"                 
#> [151] "TG(52:4)>TG(16:1_18:1_18:2)_M+NH3_feature1"                                                               
#> [152] "TG(52:4)>TG(16:1_18:1_18:2)_M+NH3_feature4"                                                               
#> [153] "TG(52:4)>TG(16:1_18:1_18:2)_M+NH3_feature5"                                                               
#> [154] "TG(52:5)>TG(16:0_18:2_18:3)_M+NH3_feature5"                                                               
#> [155] "TG(52:5)>TG(16:1_18:2_18:2)_feature3"                                                                     
#> [156] "TG(52:6)>TG(16:1_18:2_18:3)_and_TG(16:2_18:2_18:2)_feature3"                                              
#> [157] "TG(52:6)_feature4"                                                                                        
#> [158] "TG(52:7)_M+NH3_feature2"                                                                                  
#> [159] "TG(53:1)>TG(16:0_18:1_19:0)_and_TG(17:0_18:0_18:1)_M+NH3_feature4"                                        
#> [160] "TG(53:2)_feature4"                                                                                        
#> [161] "TG(53:3)>TG(17:0_18:1_18:2)_and_TG(17:1_18:1_18:1)_and_TG(16:1_18:1_19:1)_and_TG(16:0_18:1_19:2)_feature5"
#> [162] "TG(53:4)>TG(17:0_18:2_18:2)_and_TG(17:1_18:1_18:2)_M+NH3_feature3"                                        
#> [163] "TG(53:5)>TG(17:1_18:2_18:2)_feature1"                                                                     
#> [164] "TG(53:6)>TG(17:2_18:2_18:2)_and_TG(17:1_18:2_18:3)_feature1"                                              
#> [165] "TG(54:1)>TG(18:0_18:0_18:1)_and_TG(16:1_18:0_20:0)_and_TG(16:0_18:0_20:1)_M+NH13_feature4"                
#> [166] "TG(54:3)>TG(18:0_18:1_18:2)_and_TG(18:1/18:1/18:1)_and_TG(16:0_18:2_20:1)_feature9"                       
#> [167] "TG(54:3)>TG(18:1/18:1/18:1)_M+NH3_feature2"                                                               
#> [168] "TG(54:3)>TG(18:1/18:1/18:1)_M+NH3_feature3"                                                               
#> [169] "TG(54:3)>TG(18:1/18:1/18:1)_M+NH3_feature8"                                                               
#> [170] "TG(54:4)>TG(18:1_18:1_18:2)_M+NH3_feature4"                                                               
#> [171] "TG(54:4)>TG(18:1_18:1_18:2)_M+NH3_feature5"                                                               
#> [172] "TG(54:4)>TG(18:1_18:1_18:2)_and_TG(18:0_18:2_18:2)_M+NH3_feature3"                                        
#> [173] "TG(54:5)>TG(18:1_18:2_18:2)_M+NH3_feature1"                                                               
#> [174] "TG(54:5)>TG(18:1_18:2_18:2)_M+NH3_feature3"                                                               
#> [175] "TG(54:5)>TG(18:1_18:2_18:2)_M+NH3_feature4"                                                               
#> [176] "TG(54:5)>TG(18:1_18:2_18:2)_and_TG(16:0_16:0_22:5)_and_TG(16:0_18:1_20:4)_feature5"                       
#> [177] "TG(54:6)>TG(16:0_16:0_22:6)_M+NH5_feature6"                                                               
#> [178] "TG(54:6)>TG(18:2/18:2/18:2)_M+NH3_feature1"                                                               
#> [179] "TG(54:6)>TG(18:2/18:2/18:2)_and_TG(18:1_18:2_18:3)_M+NH3_feature4"                                        
#> [180] "TG(54:7)>TG(18:2_18:2_18:3)_feature2"                                                                     
#> [181] "TG(54:8)_M+NH3_feature3"                                                                                  
#> [182] "TG(54:8)_feature1"                                                                                        
#> [183] "TG(55:2)_M+NH3_feature2"                                                                                  
#> [184] "TG(55:3)>TG(18:1_18:1_19:1)_and_TG(18:1_18:2_19:0)_feature3"                                              
#> [185] "TG(55:4)>TG(18:1_18:2_19:1)_and_TG(18:2_18:2_19:0)_and_TG(18:1_18:1_19:2)_M+NH3_feature1"                 
#> [186] "TG(55:4)>TG(18:1_18:2_19:1)_and_TG(18:2_18:2_19:0)_and_TG(18:1_18:1_19:2)_feature2"                       
#> [187] "TG(55:5)>TG(18:2_18:2_19:1)_and_TG(18:1_18:2_19:2)_M+NH3_feature1"                                        
#> [188] "TG(55:5)>TG(18:2_18:2_19:1)_and_TG(18:1_18:2_19:2)_feature4"                                              
#> [189] "TG(55:7)_M+NH3_feature2"                                                                                  
#> [190] "TG(56:10)>TG(18:2_18:3_20:5)_M+NH3_feature1"                                                              
#> [191] "TG(56:4)>TG(18:1_18:2_20:1)_and_TG(18:1_18:1_20:2)_M+NH3_feature1"                                        
#> [192] "TG(56:4)>TG(18:1_18:2_20:1)_and_TG(18:1_18:1_20:2)_M+NH3_feature5"                                        
#> [193] "TG(56:4)>TG(18:1_18:2_20:1)_and_TG(18:1_18:1_20:2)_feature4"                                              
#> [194] "TG(56:5)>TG(16:0_18:1_22:4)_M+NH3_feature1"                                                               
#> [195] "TG(56:5)>TG(16:0_18:1_22:4)_M+NH3_feature4"                                                               
#> [196] "TG(56:5)>TG(16:0_18:1_22:4)_M+NH3_feature5"                                                               
#> [197] "TG(56:6)>TG(18:0_16:0_22:6)_M+NH3_feature5"                                                               
#> [198] "TG(56:6)>TG(18:1_18:1_20:4)_and_TG(16:0_18:1_22:5)_and_TG(18:1_18:2_20:3)_M+NH3_feature1"                 
#> [199] "TG(56:6)>TG(18:1_18:1_20:4)_and_TG(16:0_18:1_22:5)_and_TG(18:1_18:2_20:3)_M+NH3_feature3"                 
#> [200] "TG(56:7)>TG(16:0_18:1_22:6)_M+NH3_feature7"                                                               
#> [201] "TG(56:7)_M+NH3_feature1"                                                                                  
#> [202] "TG(56:7)_feature5"                                                                                        
#> [203] "TG(56:8)>TG(16:0_18:2_22:6)_M+NH3_feature5"                                                               
#> [204] "TG(56:8)>TG(18:2_18:2_20:4)_feature3"                                                                     
#> [205] "TG(56:9)_M+NH3_feature2"                                                                                  
#> [206] "TG(57:1)>TG(16:0_18:1_23:0)_and_TG(18:0_18:1_21:0)_M+NH3_feature1"                                        
#> [207] "TG(57:2)_M+NH3_feature1"                                                                                  
#> [208] "TG(57:3)_M+NH3_feature2"                                                                                  
#> [209] "TG(57:4)_M+NH3_feature2"                                                                                  
#> [210] "TG(57:4)_M+NH3_feature3"                                                                                  
#> [211] "TG(58:1)>TG(16:0_18:1_24:0)_and_TG(16:0_16:0_26:1)_and_TG(18:0_18:1_22:0)_M+NH3_feature1"                 
#> [212] "TG(58:10)_M+NH3_feature1"                                                                                 
#> [213] "TG(58:10)_M+NH3_feature2"                                                                                 
#> [214] "TG(58:11)_M+NH3_feature1"                                                                                 
#> [215] "TG(58:11)_M+NH3_feature2"                                                                                 
#> [216] "TG(58:2)_feature3"                                                                                        
#> [217] "TG(58:3)_M+NH3_feature1"                                                                                  
#> [218] "TG(58:4)_M+NH3_feature5"                                                                                  
#> [219] "TG(58:4)_feature6"                                                                                        
#> [220] "TG(58:5)_M+NH3_feature6"                                                                                  
#> [221] "TG(58:6)>TG(18:0_18:0_22:6)_M+NH3_feature7"                                                               
#> [222] "TG(58:6)_M+NH3_feature1"                                                                                  
#> [223] "TG(58:6)_M+NH3_feature5"                                                                                  
#> [224] "TG(58:6)_M+NH3_feature6"                                                                                  
#> [225] "TG(58:7)>TG(18:0_18:1_22:6)_M+NH3_feature5"                                                               
#> [226] "TG(58:7)>TG(18:0_18:1_22:6)_feature3"                                                                     
#> [227] "TG(58:8)>TG(18:2_18:2_22:4)_feature4"                                                                     
#> [228] "TG(58:9)_M+NH3_feature1"                                                                                  
#> [229] "TG(58:9)_M+NH3_feature2"                                                                                  
#> [230] "TG(58:9)_M+NH3_feature3"                                                                                  
#> [231] "TG(60:10)>TG(18:0_20:4_22:6)_M+NH3_feature3"                                                              
#> [232] "TG(60:10)>TG(18:0_20:4_22:6)_M+NH3_feature4"                                                              
#> [233] "TG(60:3)_M+NH3_feature2"                                                                                  
#> [234] "TG(60:4)_feature1"                                                                                        
#> [235] "ubiquinol Q9 _feature1"                                                                                   
#> [236] "CL(72:8)_feature1"                                                                                        
#> [237] "Cer(d34:1)_M+H2CO2_feature1"                                                                              
#> [238] "Cer(d36:1)_M+H2CO2_feature1"                                                                              
#> [239] "Cer(d36:2)_M+H2CO2_feature1"                                                                              
#> [240] "Cer(d40:2)_M+H2CO2_feature2"                                                                              
#> [241] "Cer(d41:2)_M+H2CO2_feature2"                                                                              
#> [242] "Cer(d42:2)_M+H2CO2_feature3"                                                                              
#> [243] "FA(22:6)_feature1"                                                                                        
#> [244] "LPE(O-15:0)_feature1"                                                                                     
#> [245] "PC(32:0)>PC(16:0_16:0)_M+H2CO2_feature2"                                                                  
#> [246] "PC(34:2)>PC(16:0_18:2)_M+H2CO2_feature1"                                                                  
#> [247] "PC(35:2)>PC(17:0_18:2)_M+H2CO2_feature2"                                                                  
#> [248] "PC(36:0)>PC(18:0/18:0)_M+H2CO2_feature3"                                                                  
#> [249] "PC(36:2)>PC(18:0_18:2)_M+H2CO2_feature3"                                                                  
#> [250] "PC(36:3)>PC(18:1_18:2)_M+H2CO2_feature2"                                                                  
#> [251] "PC(36:4)>PC(18:2/18:2)_M+H2CO2_feature2"                                                                  
#> [252] "PC(40:6)>PC(18:0_22:6) _M+H2CO2_feature3"                                                                 
#> [253] "PE(34:1)>PE(16:0_18:1)_feature1"                                                                          
#> [254] "PE(34:2)>PE(16:0_18:2)_feature2"                                                                          
#> [255] "PE(36:2)>PE(18:0_18:2)_feature2"                                                                          
#> [256] "PE(36:2)>PE(18:1/18:1)_feature2"                                                                          
#> [257] "PE(36:3)>PE(18:1_18:2)_feature1"                                                                          
#> [258] "PE(36:4)>(16:0_20:4)_feature3"                                                                            
#> [259] "PE(38:4)>PE(16:0_22:4)_feature4"                                                                          
#> [260] "PE(38:5)>PE(16:0_22:5)_and_PE(38:5)>PE(18:1_20:4)_feature3"                                               
#> [261] "PE(O-34:3)>PE(O-16:1/18:2)_feature1"                                                                      
#> [262] "PS(36:2)>PS(18:0_18:2)_feature4"                                                                          
#> [263] "PS(38:4)>PS(18:0_20:4)_feature6"                                                                          
#> [264] "SM(d40:2)_M+H2CO2_feature2"                                                                               
#> [265] "SM(d41:2)_M+H2CO2_feature1"                                                                               
#> [266] "SM(d42:2)_M+H2CO2_feature1and2"                                                                           
#> [267] "1-methylnicotinamide"                                                                                     
#> [268] "2'-deoxycytidine"                                                                                         
#> [269] "2-aminoisobutyrate"                                                                                       
#> [270] "4-aminohippurate"                                                                                         
#> [271] "4-pyridoxate"                                                                                             
#> [272] "5-methylcytidine"                                                                                         
#> [273] "7-methylguanine"                                                                                          
#> [274] "ADMA"                                                                                                     
#> [275] "C-glycosyltryptophan"                                                                                     
#> [276] "C16-OH carnitine"                                                                                         
#> [277] "C16:0 LPE"                                                                                                
#> [278] "C16:0 SM"                                                                                                 
#> [279] "C16:1 SM"                                                                                                 
#> [280] "C18:0 LPC"                                                                                                
#> [281] "C18:0 LPE A"                                                                                              
#> [282] "C18:0 SM"                                                                                                 
#> [283] "C18:1 LPC"                                                                                                
#> [284] "C18:1 LPE"                                                                                                
#> [285] "C18:1 SM"                                                                                                 
#> [286] "C18:1-OH carnitine"                                                                                       
#> [287] "C18:2 LPC"                                                                                                
#> [288] "C18:2 LPE"                                                                                                
#> [289] "C18:3 LPE"                                                                                                
#> [290] "C20:0 LPE"                                                                                                
#> [291] "C20:1 LPC"                                                                                                
#> [292] "C20:4 LPC A"                                                                                              
#> [293] "C20:4 LPC B"                                                                                              
#> [294] "C20:4 LPE"                                                                                                
#> [295] "C20:5 LPC"                                                                                                
#> [296] "C24:1 ceramide (d18:1)"                                                                                   
#> [297] "C3-DC carnitine"                                                                                          
#> [298] "C34:2 PE"                                                                                                 
#> [299] "C34:2 PE plasmalogen"                                                                                     
#> [300] "C34:3 PC plasmalogen"                                                                                     
#> [301] "C34:3 PE plasmalogen"                                                                                     
#> [302] "C36:2 PE"                                                                                                 
#> [303] "C36:3 PE plasmalogen"                                                                                     
#> [304] "C36:4 PE"                                                                                                 
#> [305] "C36:5 PE plasmalogen"                                                                                     
#> [306] "C38:4 PE"                                                                                                 
#> [307] "C38:5 PE plasmalogen"                                                                                     
#> [308] "C38:6 PE plasmalogen"                                                                                     
#> [309] "C38:7 PC plasmalogen"                                                                                     
#> [310] "L-alpha-glutamyl-L-Lysine"                                                                                
#> [311] "N-acetylaspartate"                                                                                        
#> [312] "N-acetylserotonin"                                                                                        
#> [313] "N-carbamoyl-beta-alanine"                                                                                 
#> [314] "N-lauroylglycine"                                                                                         
#> [315] "N-methylproline"                                                                                          
#> [316] "N1-methyl-2-pyridone-5-carboxamide"                                                                       
#> [317] "N6,N6-dimethyllysine"                                                                                     
#> [318] "N6-acetyllysine"                                                                                          
#> [319] "N6-methyllysine"                                                                                          
#> [320] "S-methyl-L-cysteine-S-oxide"                                                                              
#> [321] "acisoga"                                                                                                  
#> [322] "ala-ala"                                                                                                  
#> [323] "allantoin"                                                                                                
#> [324] "beta-guanidinopropionate"                                                                                 
#> [325] "betaine"                                                                                                  
#> [326] "biotin"                                                                                                   
#> [327] "creatinine"                                                                                               
#> [328] "cyclohexylamine"                                                                                          
#> [329] "cystine"                                                                                                  
#> [330] "dimethylglycine"                                                                                          
#> [331] "ectoine"                                                                                                  
#> [332] "guanidinoacetate"                                                                                         
#> [333] "imidazoleacetate"                                                                                         
#> [334] "methionine sulfoxide"                                                                                     
#> [335] "methylguanidine"                                                                                          
#> [336] "nicotinate"                                                                                               
#> [337] "oxypurinol"                                                                                               
#> [338] "pantothenol"                                                                                              
#> [339] "phenylacetylglycine"                                                                                      
#> [340] "pipecolate"                                                                                               
#> [341] "proline-betaine"                                                                                          
#> [342] "pyridoxine"                                                                                               
#> [343] "thiamine"                                                                                                 
#> [344] "vitamin A"                                                                                                
#> [345] "3-hydroxyphenyl-valerate"                                                                                 
#> [346] "Car(11:0)"                                                                                                
#> [347] "Car(16:1)"                                                                                                
#> [348] "Car(16:2)"                                                                                                
#> [349] "Car(16:3)"                                                                                                
#> [350] "Car(5:0-OH)"                                                                                              
#> [351] "Car(8:1)"                                                                                                 
#> [352] "DG(18:1_18:1)"                                                                                            
#> [353] "DG(32:0)"                                                                                                 
#> [354] "DG(32:1)"                                                                                                 
#> [355] "DG(34:2)"                                                                                                 
#> [356] "DG(36:3)"                                                                                                 
#> [357] "Glu-Phe"                                                                                                  
#> [358] "LPC(15:0)"                                                                                                
#> [359] "LPC(16:0)_a_b"                                                                                            
#> [360] "LPC(16:0)_b"                                                                                              
#> [361] "LPC(18:1)_b"                                                                                              
#> [362] "LPC(18:2)_a_b"                                                                                            
#> [363] "LPC(18:2)_b"                                                                                              
#> [364] "LPC(20:0)"                                                                                                
#> [365] "LPC(20:3)_b"                                                                                              
#> [366] "LPC(20:4)_a_b"                                                                                            
#> [367] "LPC(20:4)_b"                                                                                              
#> [368] "LPE(18:0)_b"                                                                                              
#> [369] "LPE(18:2)_b"                                                                                              
#> [370] "MG(14:0)"                                                                                                 
#> [371] "MG(16:0)"                                                                                                 
#> [372] "N-acetylneuraminate"                                                                                      
#> [373] "N-undecanoylglycine"                                                                                      
#> [374] "PC(28:0)"                                                                                                 
#> [375] "PC(32:0)"                                                                                                 
#> [376] "PC(32:1)"                                                                                                 
#> [377] "PC(33:2)"                                                                                                 
#> [378] "PC(34:2)"                                                                                                 
#> [379] "PC(35:2)"                                                                                                 
#> [380] "PC(36:3)"                                                                                                 
#> [381] "PC(36:4)"                                                                                                 
#> [382] "PC(38:6)"                                                                                                 
#> [383] "SM(d42:2)"                                                                                                
#> [384] "alpha-tocopherol"                                                                                         
#> [385] "benzylbutylphthalate"                                                                                     
#> [386] "bis(2-ethylhexyl)phthalate"                                                                               
#> [387] "cholesterol"                                                                                              
#> [388] "deoxyguanosine"                                                                                           
#> [389] "diethylphthalate"                                                                                         
#> [390] "monoethylhexyl phthalate"                                                                                 
#> [391] "oleamide"                                                                                                 
#> [392] "pyridoxamine"                                                                                             
#> [393] "sphinganine (C16)"                                                                                        
#> [394] "2-hydroxybutyrate"                                                                                        
#> [395] "3-hydroxybutyrate"                                                                                        
#> [396] "FA(14:1)"                                                                                                 
#> [397] "alpha-muricholate"                                                                                        
#> [398] "beta-muricholate"                                                                                         
#> [399] "chenodeoxycholate"                                                                                        
#> [400] "cholate"                                                                                                  
#> [401] "hydroxyindole acetate"                                                                                    
#> [402] "omega-muricholate"                                                                                        
#> [403] "tauro-alpha-muricholate"                                                                                  
#> [404] "tauro-alpha-muricholate + tauro-beta-muricholiate"                                                        
#> [405] "taurohyocoholate"                                                                                         
#> [406] "ursodeoxycholate"                                                                                         
#> [407] "N-acetyl-D-glucosamine-1-phosphate"                                                                       
#> [408] "deoxyuridine"                                                                                             
#> [409] "gluconate"                                                                                                
#> [410] "glyceraldehyde-3-phosphate"                                                                               
#> [411] "hexose"                                                                                                   
#> [412] "oxidized glutathione"                                                                                     
#> [413] "phosphoserine"                                                                                            
#> [414] "ribose 5-phosphate"                                                                                       
#> [415] "sedoheptulose-7-phosphate"                                                                                
#> 
#> $M2
#>   [1] "ADP"                                                                                    
#>   [2] "AMP"                                                                                    
#>   [3] "ATP"                                                                                    
#>   [4] "biliverdin"                                                                             
#>   [5] "C10 carnitine"                                                                          
#>   [6] "C4 carnitine"                                                                           
#>   [7] "C5 carnitine"                                                                           
#>   [8] "C5:1 carnitine"                                                                         
#>   [9] "C6 carnitine"                                                                           
#>  [10] "C8 carnitine"                                                                           
#>  [11] "cis-aconitate"                                                                          
#>  [12] "CMP"                                                                                    
#>  [13] "GDP"                                                                                    
#>  [14] "glucose"                                                                                
#>  [15] "GMP"                                                                                    
#>  [16] "IMP"                                                                                    
#>  [17] "NAD+"                                                                                   
#>  [18] "NADH"                                                                                   
#>  [19] "NADP+"                                                                                  
#>  [20] "NADPH"                                                                                  
#>  [21] "niacinamide"                                                                            
#>  [22] "pantothenate"                                                                           
#>  [23] "PC(34:3)"                                                                               
#>  [24] "PE(38:5)_feature4"                                                                      
#>  [25] "serotonin"                                                                              
#>  [26] "SM(d35:1)_feature1"                                                                     
#>  [27] "SM(d36:1)_feature1"                                                                     
#>  [28] "alpha-glycerophosphocholine"                                                            
#>  [29] "UDP"                                                                                    
#>  [30] "UMP"                                                                                    
#>  [31] "urate"                                                                                  
#>  [32] "UTP"                                                                                    
#>  [33] "CoA(2:0)"                                                                               
#>  [34] "Linoleoyl-EA"                                                                           
#>  [35] "CoA(10:0)"                                                                              
#>  [36] "CoA(10:1)"                                                                              
#>  [37] "CoA(10:3)"                                                                              
#>  [38] "CoA(11:0)"                                                                              
#>  [39] "CoA(12:0)"                                                                              
#>  [40] "CoA(12:1)"                                                                              
#>  [41] "CoA(14:0-OH)"                                                                           
#>  [42] "CoA(16:2)"                                                                              
#>  [43] "CoA(20:4)"                                                                              
#>  [44] "CoA(21:0)"                                                                              
#>  [45] "CoA(21:2)"                                                                              
#>  [46] "CoA(22:4)"                                                                              
#>  [47] "CoA(22:5)"                                                                              
#>  [48] "CoA(2:0-COOH)_and_CoA(4:0-OH)"                                                          
#>  [49] "CoA(3:0)"                                                                               
#>  [50] "CoA(3:0, 3-OH)"                                                                         
#>  [51] "CoA(3:0-COOH)"                                                                          
#>  [52] "CoA(4:0)"                                                                               
#>  [53] "CoA(4:0-CH3)"                                                                           
#>  [54] "CoA(4:0-COOH)"                                                                          
#>  [55] "CoA(4:1)"                                                                               
#>  [56] "CoA(4:1-COOH)"                                                                          
#>  [57] "CoA(6:0)"                                                                               
#>  [58] "CoA(6:1)"                                                                               
#>  [59] "CoA(8:0)"                                                                               
#>  [60] "CoA(8:1)"                                                                               
#>  [61] "CoA(9:0)"                                                                               
#>  [62] "coenzyme A"                                                                             
#>  [63] "ADP-ribose"                                                                             
#>  [64] "CDP"                                                                                    
#>  [65] "CTP"                                                                                    
#>  [66] "GDP-mannose"                                                                            
#>  [67] "GTP"                                                                                    
#>  [68] "PRPP"                                                                                   
#>  [69] "S-AMP"                                                                                  
#>  [70] "UDP-galactose"                                                                          
#>  [71] "dCTP"                                                                                   
#>  [72] "14,15-EpETrE"                                                                           
#>  [73] "20-HETE"                                                                                
#>  [74] "5,6-DiHETrE"                                                                            
#>  [75] "Resolvin D3"                                                                            
#>  [76] "Arachidonoyl-EA"                                                                        
#>  [77] "Cer(d34:0)>Cer(d18:0/16:0)_feature1"                                                    
#>  [78] "DG(32:1)>DG(16:0_16:1_0:0)_feature1"                                                    
#>  [79] "DG(34:1)>DG(16:0_18:1_0:0)_M+NH3_feature1"                                              
#>  [80] "DG(38:3)>DG(18:2_20:1_0:0)_feature2"                                                    
#>  [81] "PE(36:2)>PE(18:2_18:0)_feature3"                                                        
#>  [82] "PE(38:6)_feature2"                                                                      
#>  [83] "PE(40:5)_feature1"                                                                      
#>  [84] "PE(40:5)_feature3"                                                                      
#>  [85] "PE(40:5)_feature4"                                                                      
#>  [86] "PE(40:6)_feature2"                                                                      
#>  [87] "PE(O-34:1)_feature1"                                                                    
#>  [88] "PE(O-34:2)>PE(O-16:1/18:1)_and_PE(O-18:2/16:0)_feature1"                                
#>  [89] "PE(O-36:5)>PE(O-16:1/20:4)_feature2"                                                    
#>  [90] "PE(O-37:5)>PE(O-17:1/20:4)_feature1"                                                    
#>  [91] "PE(O-37:5)>PE(O-17:1/20:4)_feature2"                                                    
#>  [92] "PE(O-38:6)>PE(O-18:2/20:4)_and_PE(O-16:1/22:5)_feature4"                                
#>  [93] "PE(O-40:6)>PE(O-18:1/22:5)_feature4"                                                    
#>  [94] "PE(O-40:6)>PE(O-18:1/22:5)_feature5"                                                    
#>  [95] "PE(O-40:7)>PE(O-18:1/22:6)_feature7"                                                    
#>  [96] "PE(O-40:8)>PE(O-18:2/22:6)_feature2"                                                    
#>  [97] "PS(36:2)_feature2"                                                                      
#>  [98] "PS(38:3)_feature2"                                                                      
#>  [99] "SM(d34:1-OH)_feature1"                                                                  
#> [100] "SM(d38:0)_feature 2"                                                                    
#> [101] "SM(d42:1)_feature1"                                                                     
#> [102] "SM(d42:1)_feature2"                                                                     
#> [103] "SM(d42:2)_feature2"                                                                     
#> [104] "SM(d42:3)_feature1"                                                                     
#> [105] "SM(d44:1)_feature1"                                                                     
#> [106] "TG(32:0)>TG(10:0_10:0_12:0)_M+NH3_feature1"                                             
#> [107] "TG(36:1)>TG(4:0_16:0_16:1)_and_TG(2:0_16:0_18:1)_M+NH3_feature1"                        
#> [108] "TG(36:2)>TG(2:0_16:0_18:2)_feature4"                                                    
#> [109] "TG(36:2)>TG(8:0_10:0_18:2)_M+NH3_feature1"                                              
#> [110] "TG(36:3)>TG(2:0_16:1_18:2)_M+NH3_feature1"                                              
#> [111] "TG(38:0)>TG(10:0_12:0_16:0)_and_TG(10:0_10:0_18:0)_and_TG(8:0_12:0_18:0)_M+NH3_feature1"
#> [112] "TG(38:0)>TG(10:0_12:0_16:0)_and_TG(10:0_10:0_18:0)_and_TG(8:0_12:0_18:0)_M+NH3_feature2"
#> [113] "TG(38:0)>TG(10:0_12:0_16:0)_and_TG(10:0_10:0_18:0)_and_TG(8:0_12:0_18:0)_M+NH3_feature3"
#> [114] "TG(38:1)>TG(10:0_10:0_18:1)_and_TG(10:0_12:0_16:1)_and_TG(8:0_12:0_18:1)_M+NH3_feature1"
#> [115] "TG(38:1)>TG(10:0_10:0_18:1)_and_TG(10:0_12:0_16:1)_and_TG(8:0_12:0_18:1)_feature2"      
#> [116] "TG(38:1)>TG(4:0_16:0_18:1)_feature3"                                                    
#> [117] "TG(38:2)>TG(10:0_10:0_18:2)_and_TG(8:0_12:0_18:2)_feature2"                             
#> [118] "TG(38:3)>TG(4:0_16:1_18:2)_M+NH3_feature1"                                              
#> [119] "TG(38:4)>TG(2:0_18:2_18:2)_feature1"                                                    
#> [120] "TG(39:2)_M+NH3_feature1"                                                                
#> [121] "TG(40:0)_M+NH3_feature1"                                                                
#> [122] "TG(40:1)_M+NH3_feature1"                                                                
#> [123] "TG(40:1)_feature2"                                                                      
#> [124] "TG(40:1)_feature3"                                                                      
#> [125] "TG(40:2)>TG(10:0_12:0_18:2)_M+NH3_feature1"                                             
#> [126] "TG(40:2)>TG(4:0_18:1_18:1)_feature2"                                                    
#> [127] "TG(40:3)>TG(4:0_18:1_18:2)_M+NH3_feature1"                                              
#> [128] "TG(41:2)_M+NH3_feature1"                                                                
#> [129] "TG(42:0)>TG(10:0_16:0_16:0)_and_TG(12:0_14:0_16:0)_M+NH3_feature1"                      
#> [130] "TG(42:4)>TG(6:0_18:2_18:2)_feature1"                                                    
#> [131] "TG(42:4)_feature2"                                                                      
#> [132] "TG(42:6)>TG(4:0_16:0_22:6)_M+NH3_feature1"                                              
#> [133] "TG(46:1)>TG(12:0_16:0_18:1)_and_TG(10:0_18:0_18:1)_and_TG(14:0_16:0_16:1)_feature2"     
#> [134] "TG(46:2)_feature2"                                                                      
#> [135] "TG(48:3)_M+NH3_feature2"                                                                
#> [136] "TG(48:4)>TG(12:0_18:2_18:2)_M+NH3_feature1"                                             
#> [137] "TG(48:4)>TG(12:0_18:2_18:2)_feature2"                                                   
#> [138] "TG(48:5)_feature2"                                                                      
#> [139] "Cer(d42:1)_M+H2CO2_feature1"                                                            
#> [140] "Cer(d42:2)_M+H2CO2_feature4"                                                            
#> [141] "LPE(18:0/0:0)_and_LPC(0:0/18:0)_feature1and2"                                           
#> [142] "PC(32:1)_feature2"                                                                      
#> [143] "PC(34:1)>PC(16:0_18:1)_M+H2CO2_feature2"                                                
#> [144] "PC(36:1)>PC(16:0_20:1)_and_PC(18:0_18:1)_M+H2CO2_feature1"                              
#> [145] "PC(36:2)>PC(18:1/18:1)_M+H2CO2_feature2"                                                
#> [146] "PC(36:4)>PC(16:0_20:4)_M+H2CO2_feature3"                                                
#> [147] "PC(37:4)>PC(17:0_20:4)_M+H2CO2_feature3"                                                
#> [148] "PC(38:4)>PC(18:0_20:4)_M+H2CO2_feature4"                                                
#> [149] "PC(38:5)>PC(16:0_22:5)_and_PC(18:1_20:4)_M+H2CO2_feature3"                              
#> [150] "PC(O-32:1)>PC(O-16:0/16:1)_M+H2CO2_feature2"                                            
#> [151] "PC(O-36:5)>PC(O-16:1/20:4)_M+H2CO2_feature5"                                            
#> [152] "PC(O-38:5)>PC(O-18:1/20:4)_M+H2CO2_feature2"                                            
#> [153] "PE(36:1)>PE(18:0_18:1)_feature3"                                                        
#> [154] "PE(40:5)>PE(18:0_22:5)_feature3"                                                        
#> [155] "PE(O-16:1_20:4)_feature3"                                                               
#> [156] "PE(O-34:2)>PE(O-16:2/18:0)_and_PE(O-18:2/16:0)_feature2"                                
#> [157] "PE(O-34:5)>PE(O-17:1/20:4)_feature1"                                                    
#> [158] "PE(O-34:5)>PE(O-17:1/20:4)_feature2"                                                    
#> [159] "PE(O-38:7)>PE(O-18:3/20:4)_feature1"                                                    
#> [160] "PE(O-40:4)>PE(O-18:0/22:4)_feature4"                                                    
#> [161] "PG(34:1)>PG(16:0_18:1)_feature1"                                                        
#> [162] "PI(36:4)>PI(16:0_20:4)_feature1"                                                        
#> [163] "PS(O-40:7)>PS(O-18:3/22:4)_feature1"                                                    
#> [164] "PS(O-40:7)>PS(O-20:3/20:4)_feature2"                                                    
#> [165] "SM(d40:0-OH)_feature1"                                                                  
#> [166] "SM(d40:1)_M+H2CO2_feature2"                                                             
#> [167] "SM(d40:2)_M+H2CO2_feature1"                                                             
#> [168] "SM(d42:1)_M+H2CO2_feature2"                                                             
#> [169] "SM(d42:2)_M+H2CO2_feature1"                                                             
#> [170] "1-methylhistamine"                                                                      
#> [171] "21-deoxycortisol"                                                                       
#> [172] "3-methylhistidine"                                                                      
#> [173] "C14:0 SM"                                                                               
#> [174] "C16:0 LPC"                                                                              
#> [175] "C16:1 LPC plasmalogen"                                                                  
#> [176] "C18:0 LPE B"                                                                            
#> [177] "C18:3 LPC"                                                                              
#> [178] "C3-DC-CH3 carnitine"                                                                    
#> [179] "C36:5 PC plasmalogen"                                                                   
#> [180] "N-acetylhistamine"                                                                      
#> [181] "N-acetylornithine"                                                                      
#> [182] "N6,N6,N6-trimethyllysine"                                                               
#> [183] "arachidoyl ethanolamide"                                                                
#> [184] "cotinine N-oxide"                                                                       
#> [185] "histamine"                                                                              
#> [186] "hypotaurine"                                                                            
#> [187] "imidazole propionate"                                                                   
#> [188] "phosphocholine"                                                                         
#> [189] "Car(10:0-OH)"                                                                           
#> [190] "Car(3:0, 2-CH3)"                                                                        
#> [191] "Car(4:0)"                                                                               
#> [192] "Car(4:0,3-CH3)"                                                                         
#> [193] "Car(5:0)"                                                                               
#> [194] "Car(8:0-OH)"                                                                            
#> [195] "Ile-Val"                                                                                
#> [196] "Leu-Ile"                                                                                
#> [197] "PC(34:4)"                                                                               
#> [198] "Phe-Phe"                                                                                
#> [199] "Ser-Leu"                                                                                
#> [200] "gamma-glutamyltyrosine"                                                                 
#> [201] "pyroglutamate"                                                                          
#> [202] "FA(10:0-OH)"                                                                            
#> [203] "FA(12:0)"                                                                               
#> [204] "FA(12:0-OH)"                                                                            
#> [205] "FA(14:0-OH)"                                                                            
#> [206] "FA(14:2)"                                                                               
#> [207] "FA(8:0-OH)"                                                                             
#> [208] "indole lactate"                                                                         
#> [209] "indoleacrylate"                                                                         
#> [210] "phenyllactate"                                                                          
#> [211] "tauro-beta-muricholate"                                                                 
#> [212] "uridine"                                                                                
#> [213] "2-phosphoglycerate+3-phosphoglycerate"                                                  
#> [214] "6-phosphogluconate"                                                                     
#> [215] "FAD"                                                                                    
#> [216] "UDP-N-acetylglucosamine"                                                                
#> [217] "UDP-glucose"                                                                            
#> [218] "UDP-glucuronate"                                                                        
#> [219] "glycerol 3-phosphate"                                                                   
#> [220] "pyruvate"                                                                               
#> [221] "ribose 5-phosphate+ribulose 5-phosphate+xylulose 5-phosphate"                           
#> 
#> $M3
#>   [1] "Car(16:0)_feature1"                                       
#>   [2] "Car(20:4)_feature1"                                       
#>   [3] "cytidine"                                                 
#>   [4] "guanosine"                                                
#>   [5] "hypoxanthine"                                             
#>   [6] "leucine+ isoleucine"                                      
#>   [7] "LPC(16:0/0:0)_and_LPC(0:0/16:0)_feature1and2"             
#>   [8] "PC(40:8)_feature1"                                        
#>   [9] "PC(O-34:1)_feature2"                                      
#>  [10] "PE(38:4)>PE(18:0_20:4)_feature5"                          
#>  [11] "PI(38:4)>PI(18:0_20:4)_feature2"                          
#>  [12] "PS(38:4)>PS(18:0_20:4)_feature2"                          
#>  [13] "xanthosine"                                               
#>  [14] "CoA(11:2)"                                                
#>  [15] "CoA(19:1)"                                                
#>  [16] "CoA(20:1)"                                                
#>  [17] "CoA(21:1)"                                                
#>  [18] "CoA(22:3)"                                                
#>  [19] "AICAR"                                                    
#>  [20] "NMN"                                                      
#>  [21] "XMP"                                                      
#>  [22] "adenine"                                                  
#>  [23] "dATP"                                                     
#>  [24] "11,12-EpETrE"                                             
#>  [25] "13-HODE"                                                  
#>  [26] "5-HETE"                                                   
#>  [27] "9-HETE"                                                   
#>  [28] "9-HODE"                                                   
#>  [29] "2-Hydroxyglutarate"                                       
#>  [30] "Car(16:1)_feature1"                                       
#>  [31] "Car(18:1)_feature1"                                       
#>  [32] "Cer(d36:1)>Cer(d18:1/18:0)_M-H2O_feature1"                
#>  [33] "Cer(d40:2)>Cer(d18:2/22:0)_feature2"                      
#>  [34] "Cer(d41:2)>Cer(d18:2/23:0)_feature2"                      
#>  [35] "Cer(d42:2)>Cer(d18:1/24:1)_feature3"                      
#>  [36] "Cer(d42:2)>Cer(d18:2/24:0)_feature4"                      
#>  [37] "Cer(d43:1)>Cer(d18:1/25:0)_feature1and2"                  
#>  [38] "Cer(d44:3)>Cer(d18:2/26:1)_feature1"                      
#>  [39] "DG(35:4)_feature1"                                        
#>  [40] "DG(36:1)>DG(18:0_18:1_0:0)_feature2"                      
#>  [41] "DG(36:2)>DG(18:1_18:1_0:0)_M+NH3_feature3"                
#>  [42] "DG(36:3)>DG(18:1_18:2_0:0)_M+NH3_feature1"                
#>  [43] "DG(38:4)>DG(16:0_22:4_0:0)_feature4"                      
#>  [44] "DG(38:4)>DG(18:0_20:4_0:0)_feature6"                      
#>  [45] "DG(38:5)>DG(18:1_20:4_0:0)_feature2"                      
#>  [46] "DG(38:6)>DG(18:2_20:4_0:0)_feature1"                      
#>  [47] "DG(40:4)>DG(18:0_22:4_0:0)_M+NH3_feature2"                
#>  [48] "DG(40:6)>DG(18:0_22:6_0:0)_feature6"                      
#>  [49] "DG(40:7)>DG(18:1_22:6_0:0)_M+NH3_feature3"                
#>  [50] "Hex2Cer(d42:1)>Hex2Cer(d18:1/24:0)_feature1"              
#>  [51] "HexCer(d40:1)>HexCer(d18:1/22:0)_feature3"                
#>  [52] "HexCer(d40:1)>HexCer(d18:1_22:0)_feature2"                
#>  [53] "HexCer(d42:2)>HexCer(d18:1/24:1)_feature3"                
#>  [54] "LPC(17:0/0:0)_and_LPC(0:0/17:0)_feature1and2"             
#>  [55] "LPC(18:0)>LPC(18:0/0:0)_and_LPC(0:0/18:0)_feature1and2"   
#>  [56] "LPC(18:1)>LPC(18:1/0:0)_and_LPC(0:0/18:1)_feature1and2"   
#>  [57] "LPC(18:2)>LPC(18:2/0:0)_and_LPC(0:0/18:2)_feature1and2"   
#>  [58] "LPC(19:0)>LPC(0:0/19:0)_feature1"                         
#>  [59] "LPC(20:0/0:0)_and_LPC(0:0/20:0)_feature1and2"             
#>  [60] "LPC(20:1)>LPC(20:1/0:0)_and_LPC(0:0/20:1)_feature1and2"   
#>  [61] "LPC(20:4)>LPC(20:4/0:0)_and_LPC(0:0/20:4)_feature1and2"   
#>  [62] "LPE(18:0)>LPE(18:0/0:0)_and_LPE(0:0/18:0)_feature1and2"   
#>  [63] "PC(30:0)_feature2"                                        
#>  [64] "PC(31:0)_feature2"                                        
#>  [65] "PC(32:0)_feature1"                                        
#>  [66] "PC(32:0)_feature2"                                        
#>  [67] "PC(32:1)_feature1"                                        
#>  [68] "PC(32:2)_feature1"                                        
#>  [69] "PC(33:0)_feature3"                                        
#>  [70] "PC(33:1)_feature1"                                        
#>  [71] "PC(34:0)_feature4"                                        
#>  [72] "PC(34:1)_feature2"                                        
#>  [73] "PC(36:3)_feature2"                                        
#>  [74] "PC(36:4)_feature2"                                        
#>  [75] "PC(37:2)_feature2"                                        
#>  [76] "PC(38:1)_feature1"                                        
#>  [77] "PC(38:3)_feature2"                                        
#>  [78] "PC(38:3)_feature3"                                        
#>  [79] "PC(38:4)_feature4"                                        
#>  [80] "PC(38:5)_feature3"                                        
#>  [81] "PC(38:6)_feature1"                                        
#>  [82] "PC(38:6)_feature2"                                        
#>  [83] "PC(39:4)_feature3"                                        
#>  [84] "PC(39:4)_feature5"                                        
#>  [85] "PC(39:5)_feature2"                                        
#>  [86] "PC(39:5)_feature6"                                        
#>  [87] "PC(40:4)_feature2"                                        
#>  [88] "PC(40:5)_feature4"                                        
#>  [89] "PC(40:6)_feature3"                                        
#>  [90] "PC(40:7)_feature3"                                        
#>  [91] "PC(42:4)_feature4"                                        
#>  [92] "PC(O-31:0)_feature2"                                      
#>  [93] "PC(O-34:0)_feature1"                                      
#>  [94] "PC(O-36:4)_feature4"                                      
#>  [95] "PC(O-38:4)_feature4"                                      
#>  [96] "PC(O-38:4)_feature6"                                      
#>  [97] "PC(O-40:6)_feature1"                                      
#>  [98] "PC(O-40:7)_feature3"                                      
#>  [99] "PE(34:1)_feature1"                                        
#> [100] "PE(36:1)_feature3"                                        
#> [101] "PE(36:2)>PE(18:2_18:0)_feature2"                          
#> [102] "PE(36:4)_feature3"                                        
#> [103] "PE(36:5)_feature2"                                        
#> [104] "PE(38:3)>PE(18:0_20:3)_feature2"                          
#> [105] "PE(38:3)>PE(18:0_20:3)_feature3"                          
#> [106] "PE(38:4)>PE(18:0_20:4)_feature8"                          
#> [107] "PE(38:6)_feature3"                                        
#> [108] "coenzyme(Q8)_feature1"                                    
#> [109] "eucramide 2M_feature1"                                    
#> [110] "LPC(18:0/0:0)_and_LPC(0:0/18:0)_M+H2CO2_feature1and2"     
#> [111] "LPE(20:0_0:0)_and_LPE(0:0/20:0)_feature1and2"             
#> [112] "PC(32:1)>PC(14:0_18:1)_and_PC(16:0_16:1)_M+H2CO2_feature1"
#> [113] "PC(38:6)>PC(18:2_20:4)_M+H2CO2_feature1"                  
#> [114] "PC(O-38:5)>PC(O-18:1/20:4)_M+H2CO2_feature1"              
#> [115] "PE(O-40:5)>PE(O-18:1/22:4)_feature3"                      
#> [116] "PE(O-40:6)>PE(O-18:1/22:5)_feature3"                      
#> [117] "PI(38:5)>PI(18:1_20:4)_feature1"                          
#> [118] "PS(36:1)>PS(18:0_18:1)_feature1"                          
#> [119] "PS(40:4)>PS(18:0_22:4)_feature1"                          
#> [120] "PS(40:5)>PS(18:0_22:5)_feature2"                          
#> [121] "PS(O-42:7)>PS(O-20:3/22:4)_feature1"                      
#> [122] "4-guanidinobutanoate"                                     
#> [123] "C18:1 LPC plasmalogen A"                                  
#> [124] "C18:1 LPC plasmalogen B"                                  
#> [125] "C38:6 PC plasmalogen"                                     
#> [126] "C7 carnitine"                                             
#> [127] "N-alpha-acetylarginine"                                   
#> [128] "N1-acetylspermidine"                                      
#> [129] "NMMA"                                                     
#> [130] "S-adenosylmethionine"                                     
#> [131] "SDMA"                                                     
#> [132] "biopterin"                                                
#> [133] "methylimidazoleacetate"                                   
#> [134] "Car(10:1)"                                                
#> [135] "LPC(17:0)_a_b"                                            
#> [136] "uracil"                                                   
#> [137] "glutarate"                                                
#> 
#> $M4
#>  [1] "carnitine"                                                        
#>  [2] "glycocholate"                                                     
#>  [3] "hippurate"                                                        
#>  [4] "PE(O-36:5)>PE(O-16:1/20:4)_feature3"                              
#>  [5] "PE(O-38:5)>PE(O-16:1/22:4)_feature5"                              
#>  [6] "PE(O-38:5)>PE(O-18:1/20:4)_feature6"                              
#>  [7] "PE(O-38:6)>PE(O-18:2/20:4)_and_PE(O-16:1/22:5)_feature2"          
#>  [8] "PE(O-40:6)>PE(O-18:2/22:4)_feature2"                              
#>  [9] "SM(d32:1)_feature1"                                               
#> [10] "SM(d34:1)_feature1"                                               
#> [11] "SM(d36:2)_feature1"                                               
#> [12] "CoA(12:2)"                                                        
#> [13] "CoA(15:1)"                                                        
#> [14] "CoA(15:2)"                                                        
#> [15] "CoA(17:1)"                                                        
#> [16] "CoA(22:2)"                                                        
#> [17] "9,10-DiHOME"                                                      
#> [18] "PGE2"                                                             
#> [19] "PC(O-38:5)_feature3"                                              
#> [20] "PC(O-38:7)_feature1"                                              
#> [21] "PE(36:4)_feature1"                                                
#> [22] "PE(40:8)_feature1"                                                
#> [23] "PE(O-36:2)>PE(O-18:1/18:1)_feature2"                              
#> [24] "PE(O-36:3)>PE(O-18:2/18:1)_feature4"                              
#> [25] "PE(O-36:3)_feature2"                                              
#> [26] "PE(O-38:4)_feature4"                                              
#> [27] "PE(O-38:5)_feature3"                                              
#> [28] "PE(O-38:7)>PE(O-16:1/22:6)_feature2"                              
#> [29] "PE(O-40:5)>PE(O-18:1/22:4)_feature4"                              
#> [30] "PE(O-40:5)>PE(O-18:1/22:4)_feature5"                              
#> [31] "PS(36:1)_feature1"                                                
#> [32] "PS(36:2)_feature3"                                                
#> [33] "PS(40:5)_feature2"                                                
#> [34] "SM(d33:1)_feature1"                                               
#> [35] "SM(d37:1)_feature1"                                               
#> [36] "SM(d38:2)_feature2"                                               
#> [37] "SM(d40:0)_feature1"                                               
#> [38] "SM(d40:1)_feature2"                                               
#> [39] "SM(d40:2)_feature1"                                               
#> [40] "SM(d40:2)_feature2"                                               
#> [41] "SM(d41:0)_feature1"                                               
#> [42] "SM(d41:2)_feature1"                                               
#> [43] "SM(d41:2)_feature2"                                               
#> [44] "SM(d41:2)_feature3"                                               
#> [45] "SM(d43:1)_feature2"                                               
#> [46] "SM(d44:3)_feature1"                                               
#> [47] "TG(30:0)>TG(10:0/10:0/10:0)_and_TG(8:0_10:0_12:0)_M+NH3_feature1" 
#> [48] "TG(34:0)>TG(10:0_10:0_14:0)_and_TG(10:0_12:0_12:0)_M+NH3_feature1"
#> [49] "TG(34:0)>TG(4:0_14:0_16:0)_M+NH3_feature3"                        
#> [50] "TG(36:0)>TG(10:0_10:0_16:0)_M+NH3_feature2"                       
#> [51] "TG(36:0)>TG(4:0_16:0_16:0)_M+NH3_feature4"                        
#> [52] "TG(40:0)_M+NH3_feature2"                                          
#> [53] "TG(40:3)>TG(4:0_18:1_18:2)_feature2"                              
#> [54] "sn-glycero-3-phosphocholine"                                      
#> [55] "Cer(d41:1)_M+H2CO2_feature1"                                      
#> [56] "Hex2Cer(d40:3)_feature1"                                          
#> [57] "HexCer(d41:1-OH)_M+H2CO2_feature1"                                
#> [58] "HexCer(d41:1-OH)_M+H2CO2_feature2"                                
#> [59] "PC(38:3)>PC(18:0_20:3)_M+H2CO2_feature3"                          
#> [60] "PE(38:6)>PE(16:0_22:6)_feature3"                                  
#> [61] "PE(40:7)>PE(18:1_22:6)_and_PE(18:0_22:7)_feature3"                
#> [62] "PE(O-38:7)>PE(O-16:1/22:6)_and_PE(O-20:7/18:0)_feature2"          
#> [63] "1-methyladenosine"                                                
#> [64] "5-methylcytosine"                                                 
#> [65] "C20:0 SM"                                                         
#> [66] "C22:0 SM"                                                         
#> [67] "C22:1 SM"                                                         
#> [68] "C22:6 LPE"                                                        
#> [69] "C24:0 LPC"                                                        
#> [70] "C34:0 PE"                                                         
#> [71] "C36:2 PS plasmalogen"                                             
#> [72] "C38:6 PE"                                                         
#> [73] "C38:7 PE plasmalogen"                                             
#> [74] "C40:6 PE"                                                         
#> [75] "C40:7 PE plasmalogen"                                             
#> [76] "N-acetylputrescine"                                               
#> [77] "N4-acetylcytidine"                                                
#> [78] "acetylcholine"                                                    
#> [79] "putrescine"                                                       
#> [80] "trigonelline"                                                     
#> [81] "trimethylamine-N-oxide"                                           
#> [82] "Ile-Pro"                                                          
#> [83] "Leu-Pro"                                                          
#> [84] "PC(34:1)"                                                         
#> [85] "PC(40:6)"                                                         
#> [86] "SM(d40:1)"                                                        
#> [87] "SM(d42:1)"                                                        
#> [88] "FA(16:0-COOH)"                                                    
#> [89] "FA(16:0-OH)"                                                      
#> [90] "FA(18:4)"                                                         
#> [91] "N-acetylphenylalanine"                                            
#> [92] "glycochenodeoxycholate"                                           
#> [93] "glycohyocholate"                                                  
#> [94] "hydroxyphenyllactic acid"                                         
#> [95] "maleate"                                                          
#> [96] "fructose 1,6-biphosphate"                                         
#> [97] "fructose 6-phosphate"                                             
#> [98] "hexose phosphate"                                                 
#> [99] "phosphocreatine"                                                  
#> 
#> $M5
#>  [1] "Car(18:0)_feature1"                                      
#>  [2] "C4-OH carnitine"                                         
#>  [3] "gamma-glutamylisoleucine"                                
#>  [4] "LPC(14:0)"                                               
#>  [5] "LPC(16:1)_a_b"                                           
#>  [6] "PC(40:5)_feature3"                                       
#>  [7] "PC(O-32:0)_feature1"                                     
#>  [8] "PE(40:4)>PE(18:0_22:4)_feature2"                         
#>  [9] "sphingosine"                                             
#> [10] "Phosphoethanolamine"                                     
#> [11] "CoA(15:0)_and_CoA(C14:1-OH)"                             
#> [12] "14,15-DiHETrE"                                           
#> [13] "Isocitrate"                                              
#> [14] "Cer(d42:3)_feature2"                                     
#> [15] "DG(32:0)>DG(16:0_16:0_0:0)_M+NH3_feature1"               
#> [16] "DG(32:0)>DG(16:0_16:0_0:0)_M+NH3_feature2"               
#> [17] "DG(34:1)>DG(16:0_18:1_0:0)_M+NH3_feature2"               
#> [18] "DG(36:1)>DG(18:0_18:1_0:0)_M+NH3_feature1"               
#> [19] "DG(36:2)>DG(18:0_18:2_0:0)_M+NH3_feature2"               
#> [20] "DG(36:3)>DG(18:1_18:2_0:0)_M+NH3_feature2"               
#> [21] "DG(36:4)>DG(16:0_20:4_0:0)_M+NH3_feature2"               
#> [22] "DG(40:4)>DG(18:0_22:4_0:0)_M+NH3_feature3"               
#> [23] "EA(15:0)_feature1"                                       
#> [24] "EA(17:0)_feature1"                                       
#> [25] "EA(18:0)_feature1"                                       
#> [26] "EA(22:0)_feature1"                                       
#> [27] "HexCer(d40:1-OH)>HexCer(d18:1/22:0-OH)_feature2"         
#> [28] "HexCer(d40:2)>HexCer(d18:1/22:1)_feature3"               
#> [29] "HexCer(d42:1)>HexCer(d18:1/24:0)_feature1"               
#> [30] "PC(34:2)_feature1"                                       
#> [31] "PC(34:3)_feature3"                                       
#> [32] "PC(35:1)_feature1"                                       
#> [33] "PC(35:2)_feature1"                                       
#> [34] "PC(35:4)_feature2"                                       
#> [35] "PC(36:2)_M+Na_feature2"                                  
#> [36] "PC(36:3)_feature1"                                       
#> [37] "PC(36:3)_feature3"                                       
#> [38] "PC(36:5)_feature3"                                       
#> [39] "PC(37:1)_feature3"                                       
#> [40] "PC(37:4)_feature3"                                       
#> [41] "PC(37:4)_feature4"                                       
#> [42] "PC(38:2)_feature3"                                       
#> [43] "PC(38:2)_feature5"                                       
#> [44] "PC(38:3)_feature4"                                       
#> [45] "PC(40:2)_feature2"                                       
#> [46] "PC(40:5)_feature1"                                       
#> [47] "PC(40:6)_feature2"                                       
#> [48] "PC(40:7)_feature2"                                       
#> [49] "PC(42:5)_feature6"                                       
#> [50] "PC(42:8)_feature2"                                       
#> [51] "PC(O-30:0)_feature1"                                     
#> [52] "PC(O-32:1)_feature2"                                     
#> [53] "PC(O-34:2)_feature1"                                     
#> [54] "PC(O-36:1)_feature3"                                     
#> [55] "PC(O-36:2)_feature1"                                     
#> [56] "PC(O-36:3)_feature1"                                     
#> [57] "PC(O-36:4)_feature2"                                     
#> [58] "PC(O-36:5)_feature5"                                     
#> [59] "PC(O-38:2)_feature3"                                     
#> [60] "PC(O-38:5)_feature1"                                     
#> [61] "PC(O-38:6)_feature2"                                     
#> [62] "PC(O-38:7)_feature2"                                     
#> [63] "PE(36:3)_feature1"                                       
#> [64] "PE(38:5)>PE(18:1_20:4)_feature3"                         
#> [65] "Cholesterol sulfate_feature1"                            
#> [66] "HexCer(d40:1)_M+H2CO2_feature2"                          
#> [67] "HexCer(d42:1)_M+H2CO2_feature2"                          
#> [68] "HexCer(d42:2)_M+H2CO2_feature3"                          
#> [69] "PE(40:6)>PE(18:0_22:6)_feature2"                         
#> [70] "PE(O-36:3)>PE(O-18:1/18:2)_feature6"                     
#> [71] "PE(O-36:3)>PE(O-18:2/18:1)_feature3"                     
#> [72] "PE(O-36:4)>PE(O-18:2/18:2)_feature1"                     
#> [73] "PE(O-36:4)>PE(O-18:3/18:1)_feature6"                     
#> [74] "PE(O-40:7)>PE(O-18:1/22:6)_and_PE(O-22:7/18:0)_feature10"
#> [75] "PE(O-40:8)>PE(O-22:8/18:0)_and_PE(O-18:2/22:6)_feature2" 
#> [76] "SM(d38:1)_M+H2CO2_feature2"                              
#> [77] "N-acetylhistidine"                                       
#> [78] "butyrobetaine"                                           
#> [79] "phytosphingosine"                                        
#> [80] "3-indolepropionate"                                      
#> [81] "FA(12:0-NH2)"                                            
#> [82] "Ile-Ile"                                                 
#> [83] "N-gammaglutamylmethionine"                               
#> [84] "bilirubin"                                               
#> [85] "kynurenine"                                              
#> [86] "citrate+isocitrate"                                      
#> 
#> $M6
#>  [1] "3-methyl-2-oxovalerate"     "5'-methylthioadenosine"    
#>  [3] "Alanine"                    "Arginine"                  
#>  [5] "Asparagine"                 "Aspartic Acid"             
#>  [7] "beta-Alanine"               "Citrate"                   
#>  [9] "Citrulline"                 "Fumarate"                  
#> [11] "gamma-Amino-N-butyric-acid" "Glutamic Acid"             
#> [13] "Glutamine"                  "Glycine"                   
#> [15] "guanine"                    "Histidine"                 
#> [17] "Hydroxyproline"             "Isoleucine"                
#> [19] "ketoleucine"                "Lactate"                   
#> [21] "Leucine"                    "Malate"                    
#> [23] "Methionine"                 "Ornithine"                 
#> [25] "Phenylalanine"              "Proline"                   
#> [27] "S-allylcysteine"            "Serine"                    
#> [29] "Succinate"                  "Taurine"                   
#> [31] "Threonine"                  "Tryptophan"                
#> [33] "Tyrosine"                   "Valine"                    
#> [35] "Lysine"                     "1-Methylhistidine"         
#> [37] "Cystathionine 1"            "Cysteine"                  
#> [39] "Ethanolamine"               "Sarcosine"                 
#> [41] "alpha-Aminoadipic-acid"     "CoA(11:1)"                 
#> [43] "CoA(13:0)"                  "CoA(14:0)"                 
#> [45] "CoA(14:1)"                  "CoA(14:2)"                 
#> [47] "CoA(16:3)"                  "CoA(18:0)"                 
#> [49] "CoA(18:1)"                  "CoA(18:2)"                 
#> [51] "CoA(18:3)"                  "CoA(19:0)"                 
#> [53] "CoA(19:2)"                  "CoA(20:0)"                 
#> [55] "CoA(20:2)"                  "CoA(20:3)"                 
#> [57] "CoA(22:1)"                  "CoA(22:6)"                 
#> [59] "CoA(4:1-CH3)"               "S-adenosylhomocysteine"    
#> [61] "11,12-DiHETrE"              "12-HETE"                   
#> [63] "8,9-EpETrE"                 "ketoisovalerate"           
#> [65] "Ketoglutarate"              "SM(d42:3)_M+H2CO2_feature1"
#> [67] "MG(18:1)_a_b"               "MG(18:1)_b"                
#> [69] "glycodeoxycholate"

lengths(METAB_MOD_LIST)
#>  M1  M2  M3  M4  M5  M6  M7 
#> 415 221 137  99  86  69  30
#  M1  M2  M3  M4  M5  M6  M7
# 415 221 137  99  86  69  30

# all features (excluding those 6 from M0)
METAB_UNIVERSE <- unique(unlist(METAB_MOD_LIST))
head(METAB_UNIVERSE)
#> [1] "adenosine"       "Anserine"        "C12 carnitine"   "C12:1 carnitine"
#> [5] "C14 carnitine"   "C14:1 carnitine"

# Reformat fData for use with fora2
REFMET_SUBCLASSES <- pluck(METAB_WGCNA, "modules") %>%
  filter(moduleColor != "grey") %>%
  group_by(refmet_sub_class) %>%
  summarise(feature = list(feature_ID)) %>%
  mutate(gs_subcat = "refmet_sub_class",
         gs_exact_source = refmet_sub_class,
         gs_description = refmet_sub_class,
         set_size = lengths(feature)) %>%
  filter(set_size >= 10)

# How many sets to test?
length(REFMET_SUBCLASSES) # Only 6
#> [1] 6
# ORA
METAB_MODULE_ORA <- fora2(pathways = REFMET_SUBCLASSES,
                          genes = METAB_MOD_LIST,
                          gene_column = "feature",
                          universe = METAB_UNIVERSE,
                          adjust.method = "scale",
                          adjust.globally = TRUE) %>%
  relocate(module, gs_subcat, pathway, gs_description) %>%
  relocate(overlap, maxOverlap, overlapRatio, .after = size) %>%
  dplyr::rename(refmet_sub_class = pathway,
                overlapMetabolites = overlapGenes) %>%
  dplyr::select(-starts_with("gs_"))

head(METAB_MODULE_ORA)
#>    module refmet_sub_class         pval         padj  size overlap maxOverlap
#>    <fctr>           <char>        <num>        <num> <int>   <int>      <int>
#> 1:     M1              TAG 5.065558e-35 8.545726e-35   190     150        150
#> 2:     M1              LPC 4.835315e-02 6.830682e-01    35      19        150
#> 3:     M1  Acyl carnitines 1.657193e-01 7.881443e-01    42      20        150
#> 4:     M1   C24 bile acids 5.010514e-02 8.201617e-01    16      10        150
#> 5:     M1              LPE 5.067624e-02 8.371493e-01    14       9        150
#> 6:     M1              Cer 1.434423e-01 8.570003e-01    23      12        150
#>    overlapRatio overlapMetabolites
#>           <num>             <list>
#> 1:   0.99337748       TG(36:1)....
#> 2:   0.12582781       LPC(20:3....
#> 3:   0.13245033       C12 carn....
#> 4:   0.06622517       deoxycho....
#> 5:   0.05960265       C16:0 LP....
#> 6:   0.07947020       Cer(d34:....
# Save
usethis::use_data(PROT_MODULE_ORA, internal = FALSE, overwrite = TRUE,
                  version = 3, compress = "bzip2")

usethis::use_data(TRNSCRPT_MODULE_ORA, internal = FALSE, overwrite = TRUE,
                  version = 3, compress = "bzip2")

usethis::use_data(METAB_MODULE_ORA, internal = FALSE, overwrite = TRUE,
                  version = 3, compress = "bzip2")

Session Info

sessionInfo()
#> R version 4.4.0 (2024-04-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] purrr_1.0.2                        tibble_3.2.1                      
#> [3] tidyr_1.3.1                        dplyr_1.1.4                       
#> [5] MotrpacRatTraining6moWAT_1.0.1     Biobase_2.64.0                    
#> [7] BiocGenerics_0.50.0                MotrpacRatTraining6moWATData_2.0.0
#> 
#> loaded via a namespace (and not attached):
#>   [1] RColorBrewer_1.1-3      rstudioapi_0.16.0       jsonlite_1.8.8         
#>   [4] shape_1.4.6.1           magrittr_2.0.3          ggbeeswarm_0.7.2       
#>   [7] rmarkdown_2.26          GlobalOptions_0.1.2     fs_1.6.4               
#>  [10] zlibbioc_1.50.0         ragg_1.3.0              vctrs_0.6.5            
#>  [13] memoise_2.0.1           base64enc_0.1-3         rstatix_0.7.2          
#>  [16] htmltools_0.5.8.1       dynamicTreeCut_1.63-1   curl_5.2.1             
#>  [19] broom_1.0.5             Formula_1.2-5           sass_0.4.9             
#>  [22] bslib_0.7.0             htmlwidgets_1.6.4       desc_1.4.3             
#>  [25] impute_1.78.0           cachem_1.0.8            lifecycle_1.0.4        
#>  [28] iterators_1.0.14        pkgconfig_2.0.3         Matrix_1.7-0           
#>  [31] R6_2.5.1                fastmap_1.1.1           GenomeInfoDbData_1.2.12
#>  [34] clue_0.3-65             digest_0.6.35           colorspace_2.1-0       
#>  [37] patchwork_1.2.0         AnnotationDbi_1.65.2    S4Vectors_0.42.0       
#>  [40] textshaping_0.3.7       Hmisc_5.1-2             RSQLite_2.3.6          
#>  [43] ggpubr_0.6.0            filelock_1.0.3          latex2exp_0.9.6        
#>  [46] fansi_1.0.6             httr_1.4.7              abind_1.4-5            
#>  [49] compiler_4.4.0          withr_3.0.0             bit64_4.0.5            
#>  [52] doParallel_1.0.17       htmlTable_2.4.2         backports_1.4.1        
#>  [55] BiocParallel_1.38.0     carData_3.0-5           DBI_1.2.2              
#>  [58] ggsignif_0.6.4          rjson_0.2.21            tools_4.4.0            
#>  [61] vipor_0.4.7             foreign_0.8-86          beeswarm_0.4.0         
#>  [64] msigdbr_7.5.1           nnet_7.3-19             glue_1.7.0             
#>  [67] grid_4.4.0              checkmate_2.3.1         cluster_2.1.6          
#>  [70] fgsea_1.30.0            generics_0.1.3          gtable_0.3.5           
#>  [73] preprocessCore_1.66.0   data.table_1.15.4       WGCNA_1.72-5           
#>  [76] car_3.1-2               utf8_1.2.4              XVector_0.44.0         
#>  [79] foreach_1.5.2           pillar_1.9.0            stringr_1.5.1          
#>  [82] babelgene_22.9          limma_3.60.0            circlize_0.4.16        
#>  [85] splines_4.4.0           BiocFileCache_2.12.0    lattice_0.22-6         
#>  [88] survival_3.5-8          bit_4.0.5               tidyselect_1.2.1       
#>  [91] GO.db_3.19.1            ComplexHeatmap_2.20.0   locfit_1.5-9.9         
#>  [94] Biostrings_2.72.0       knitr_1.46              gridExtra_2.3          
#>  [97] IRanges_2.38.0          edgeR_4.2.0             stats4_4.4.0           
#> [100] xfun_0.43               statmod_1.5.0           matrixStats_1.3.0      
#> [103] stringi_1.8.3           UCSC.utils_1.0.0        yaml_2.3.8             
#> [106] evaluate_0.23           codetools_0.2-20        cli_3.6.2              
#> [109] ontologyIndex_2.12      rpart_4.1.23            systemfonts_1.0.6      
#> [112] munsell_0.5.1           jquerylib_0.1.4         Rcpp_1.0.12            
#> [115] GenomeInfoDb_1.40.0     dbplyr_2.5.0            png_0.1-8              
#> [118] fastcluster_1.2.6       parallel_4.4.0          pkgdown_2.0.9          
#> [121] ggplot2_3.5.1           blob_1.2.4              scales_1.3.0           
#> [124] crayon_1.5.2            GetoptLong_1.0.5        rlang_1.1.3            
#> [127] cowplot_1.1.3           fastmatch_1.1-4         KEGGREST_1.44.0