p.matrix: Assembles a matrix of nominal or adjusted pvalues from a...

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

Description

You might want a matrix of pvalues (or FDRs) for the gene sets across all GSEA methods you tried. I think I did, once, so here it is.

Usage

p.matrix(
  x,
  names = resultNames(x),
  pcol = c("padj", "padj.by.collection", "pval")
)

Arguments

x	A MultiGSEAResult() object.
names	the entries from resultNames(x) that you want to include in the matrix. By default we take all of them.
pval	Are we testing pvalues or adjusted pvalues?

Value

A matrix of the desired pvalues for all genesets

Examples

# vm <- exampleExpressionSet(do.voom=TRUE)
# gdb <- exampleGeneSetDb()
# mg <- multiGSEA(gdb, vm, vm$design, 'tumor', methods=c('cameraPR'))
mg <- exampleMultiGSEAResult()
pm <- p.matrix(mg)

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