Enriched pathways from gene set collections

enrichedGeneSets(object, ...)

# S4 method for FGSEAList
enrichedGeneSets(object, collection,
  flatten = TRUE)

Arguments

object

Object.

collection

character(1). Gene set collection name. Typically refers to h, c1-c7 collections from MSigDb. Can obtain using collectionNames() on FGSEAList object.

flatten

logical(1). Flatten nested "up"/"down" directional enrichment vector subsets. Recomended by default for UpSet plots.

...

Additional arguments.

Value

list. Named list formatted as:

  1. Gene set collection (e.g. "h" from MSigDb).

  2. Contrast (e.g. "dmso_r1881_vs_etoh").

  3. Direction (e.g. "down" or "up").

Examples

data(gsea) enrichedGeneSets(gsea, collection = "h")
#> $dmso_r1881_vs_etoh_down #> [1] "HALLMARK_INTERFERON_ALPHA_RESPONSE" "HALLMARK_MYOGENESIS" #> [3] "HALLMARK_HEDGEHOG_SIGNALING" "HALLMARK_HEME_METABOLISM" #> [5] "HALLMARK_COAGULATION" "HALLMARK_UV_RESPONSE_DN" #> [7] "HALLMARK_COMPLEMENT" "HALLMARK_APICAL_JUNCTION" #> #> $dmso_r1881_vs_etoh_up #> [1] "HALLMARK_E2F_TARGETS" "HALLMARK_MYC_TARGETS_V1" #> [3] "HALLMARK_ANDROGEN_RESPONSE" "HALLMARK_G2M_CHECKPOINT" #> [5] "HALLMARK_MYC_TARGETS_V2" "HALLMARK_MTORC1_SIGNALING" #> [7] "HALLMARK_DNA_REPAIR" "HALLMARK_UNFOLDED_PROTEIN_RESPONSE" #> [9] "HALLMARK_MITOTIC_SPINDLE" "HALLMARK_ESTROGEN_RESPONSE_LATE" #> [11] "HALLMARK_UV_RESPONSE_UP" "HALLMARK_GLYCOLYSIS" #> [13] "HALLMARK_CHOLESTEROL_HOMEOSTASIS" "HALLMARK_FATTY_ACID_METABOLISM" #> [15] "HALLMARK_ESTROGEN_RESPONSE_EARLY" "HALLMARK_SPERMATOGENESIS" #> [17] "HALLMARK_PEROXISOME" "HALLMARK_XENOBIOTIC_METABOLISM" #> [19] "HALLMARK_OXIDATIVE_PHOSPHORYLATION" "HALLMARK_IL2_STAT5_SIGNALING" #>