rliger (version 1.0.0)

runGSEA: 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

# NOT RUN {
# ligerex (liger object), factorization complete
wilcox.results <- runGSEA(ligerex)
wilcox.results <- runGSEA(ligerex, mat_v = c(1, 2))
# }
# NOT RUN {
# }