vignettes/WGCNA_MODULE_ORA.Rmd
WGCNA_MODULE_ORA.Rmd
library(MotrpacRatTraining6moWATData)
library(MotrpacRatTraining6moWAT)
library(dplyr)
library(tidyr)
library(tibble)
library(purrr)
# 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....
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....
# 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")
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