geneSetSummaryByGenes: Summarize geneset:feature relationships for specified set of...

In lianos/multiGSEA: A unified interface to a plethora of gene set enrichment analysis methods

Description

This function creates a geneset by feature table with geneset membership information for a specified feature set. Only the gene sets that have any of the features are included.

Usage

geneSetSummaryByGenes(
  x,
  features,
  with.features = TRUE,
  feature.rename = NULL,
  ...
)

## S4 method for signature 'GeneSetDb'
geneSetSummaryByGenes(
  x,
  features,
  with.features = TRUE,
  feature.rename = NULL,
  ...,
  as.dt = FALSE
)

## S4 method for signature 'MultiGSEAResult'
geneSetSummaryByGenes(
  x,
  features,
  with.features = TRUE,
  feature.rename = NULL,
  method = NULL,
  max.p = 0.3,
  p.col = c("padj", "padj.by.collection", "pval"),
  ...,
  as.dt = FALSE
)

Arguments

x	GeneSetDb or MultiGSEAResult
features	a character vector of featureIds
with.features	Include columns for features? If x is is a GeneSetDb, these columns are TRUE/FALSE. If x is a MultiGSEAResult object, the values are the logFC of the feature if present in the gene set, otherwise its NA.
feature.rename	if NULL, the feature columns are prefixed with featureId_, if FALSE, no renaming is done. If x is a MultiGSEAResult, then this can be the column name found in logFC(x), in which case the value for the feature from the given column name would be used (setting this to "symbol") would be a common thing to do, for instance.

Value

a data.frame of geneset <-> feature incidence/feature matrix.

Examples

vm <- exampleExpressionSet(do.voom=TRUE)
gdb <- conform(exampleGeneSetDb(), vm)
mg <- multiGSEA(gdb, vm, vm$design, 'tumor', methods=NULL)
features <- c("55839", "8522", "29087")
gsm.hit <- geneSetSummaryByGenes(gdb, features)
gsm.fid <- geneSetSummaryByGenes(mg, features, feature.rename=NULL)
gsm.sym <- geneSetSummaryByGenes(mg, features, feature.rename='symbol')

lianos/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.