Remove all non-empty trajectories

Usage

get_all_trajectories(
  edge_sets = MotrpacRatTraining6moData::GRAPH_COMPONENTS$edge_sets,
  node_sets = MotrpacRatTraining6moData::GRAPH_COMPONENTS$node_sets,
  tissues = MotrpacRatTraining6moData::TISSUE_ABBREV,
  omes = MotrpacRatTraining6moData::ASSAY_ABBREV
)

Arguments

edge_sets: A named list with the edge (state) sets of analytes/features. GRAPH_COMPONENTS$edge_sets by default.
node_sets: A named list with the node (state) sets of analytes/features. GRAPH_COMPONENTS$node_sets by default.
tissues: string vector, optional. tissue subset. all tissues by default
omes: string vector, optional. ome subset. all omes by default

Value

named list with one element per trajectories. members are features in the path

Examples

# Get lists of features belonging to all trajectories in the liver
liver = get_all_trajectories(tissues = "LIVER")
lapply(liver[1:5], head)
#> $`1w_F0_M1->2w_F0_M1->4w_F0_M1->8w_F1_M1`
#> [1] "ACETYL;LIVER;AP_004896.1_K54k"     "ACETYL;LIVER;NP_001004258.1_K350k"
#> [3] "ACETYL;LIVER;NP_001006971.1_K41k"  "ACETYL;LIVER;NP_001006971.1_K434k"
#> [5] "ACETYL;LIVER;NP_001006982.2_K278k" "ACETYL;LIVER;NP_001006982.2_K441k"
#> 
#> $`1w_F0_M0->2w_F0_M0->4w_F0_M0->8w_F1_M1`
#> [1] "ACETYL;LIVER;NP_001004250.1_K85k"  "ACETYL;LIVER;NP_001007667.1_K213k"
#> [3] "ACETYL;LIVER;NP_001007804.1_K126k" "ACETYL;LIVER;NP_001013175.1_K224k"
#> [5] "ACETYL;LIVER;NP_001014183.1_K106k" "ACETYL;LIVER;NP_001014183.1_K155k"
#> 
#> $`1w_F0_M0->2w_F0_M0->4w_F0_M0->8w_F-1_M-1`
#> [1] "ACETYL;LIVER;NP_001009706.1_K59k"  "ACETYL;LIVER;NP_001014157.1_K569k"
#> [3] "ACETYL;LIVER;NP_001014262.3_K171k" "ACETYL;LIVER;NP_001014262.3_K246k"
#> [5] "ACETYL;LIVER;NP_001014262.3_K75k"  "ACETYL;LIVER;NP_001041307.1_K648k"
#> 
#> $`1w_F1_M1->2w_F1_M1->4w_F1_M1->8w_F1_M1`
#> [1] "ACETYL;LIVER;NP_001013175.1_K397k" "ACETYL;LIVER;NP_001014181.2_K32k" 
#> [3] "ACETYL;LIVER;NP_001094009.1_K125k" "ACETYL;LIVER;NP_001101972.2_K531k"
#> [5] "ACETYL;LIVER;NP_001101972.2_K538k" "ACETYL;LIVER;NP_001101972.2_K545k"
#> 
#> $`1w_F0_M0->2w_F0_M0->4w_F0_M0->8w_F0_M-1`
#> [1] "ACETYL;LIVER;NP_001012177.1_K141k" "ACETYL;LIVER;NP_001014262.3_K68k" 
#> [3] "ACETYL;LIVER;NP_001093972.1_K578k" "ACETYL;LIVER;NP_001102492.1_K211k"
#> [5] "ACETYL;LIVER;NP_001102492.1_K97k"  "ACETYL;LIVER;NP_001102560.1_K215k"
#>