runGSEA: Analyze biological interpretations of metagene

In rliger: Linked Inference of Genomic Experimental Relationships

Analyze biological interpretations of metagene

Description

Identify the biological pathways (gene sets from Reactome) that each metagene (factor) might belongs to.

Usage

runGSEA(
  object,
  gene_sets = c(),
  mat_w = TRUE,
  mat_v = 0,
  custom_gene_sets = c()
)

Arguments

object	liger object.
gene_sets	A list of the Reactome gene sets names to be tested. If not specified, this function will use all the gene sets from the Reactome by default
mat_w	This indicates whether to use the shared factor loadings 'W' (default TRUE)
mat_v	This indicates which V matrix to be added to the analysis. It can be a numeric number or a list of the numerics.
custom_gene_sets	A named list of character vectors of entrez gene ids. If not specified, this function will use all the gene symbols from the input matrix by default

Value

A list of matrices with GSEA analysis for each factor

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
# Specification for minimal example run time, not converging
ligerex <- optimizeALS(ligerex, k = 5, max.iters = 1)
result <- runGSEA(ligerex)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.