getPatternGeneSet-methods: generate statistics associating patterns with gene sets

In CoGAPS/CoGAPS: Coordinated Gene Activity in Pattern Sets

generate statistics associating patterns with gene sets

Description

generate statistics associating patterns with gene sets

Usage

getPatternGeneSet(
  object,
  gene.sets,
  method = c("enrichment", "overrepresentation"),
  ...
)

## S4 method for signature 'CogapsResult,list,character'
getPatternGeneSet(
  object,
  gene.sets,
  method = c("enrichment", "overrepresentation"),
  ...
)

Arguments

object	an object of type CogapsResult
gene.sets	a list of gene sets to test. List names should be the names of the gene sets
method	enrichment or overrepresentation. Conducts a test for gene set enrichment using fgsea::gsea ranking features by pattern amplitude or a test for gene set overrepresentation in pattern markers using fgsea::fora, respectively.
...	additional parameters passed to patternMarkers if using overrepresentation method

Value

list of dataframes containing gene set enrichment or gene set overrepresentation statistics

Examples

data(GIST)
gs.test <- list(
"gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
"gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
)
getPatternGeneSet(object = GIST.result, gene.sets = gs.test, method = "enrichment")
getPatternGeneSet(object = GIST.result, gene.sets = gs.test, method = "overrepresentation")

CoGAPS/CoGAPS documentation built on April 12, 2024, 3:12 a.m.