runGSEA {rliger}

Analyze biological interpretations of metagene

Description

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

Usage

runGSEA(
  object,
  genesets = NULL,
  useW = TRUE,
  useV = NULL,
  customGenesets = NULL,
  gene_sets = genesets,
  mat_w = useW,
  mat_v = useV,
  custom_gene_sets = customGenesets
)

Arguments

object

A liger object with valid factorization result.

genesets

Character vector of the Reactome gene sets names to be tested. Default NULL uses all the gene sets from the Reactome.

useW

Logical, whether to use the shared factor loadings (W). Default TRUE.

useV

A character vector of the names, a numeric or logical vector of the index of the datasets where the V matrices will be included for analysis. Default NULL uses all datasets.

customGenesets

A named list of character vectors of entrez gene ids. Default NULL uses all the gene symbols from the input matrix.

gene_sets, mat_w, mat_v, custom_gene_sets

Deprecated. See Usage section for replacement.

Value

A list of matrices with GSEA analysis for each factor

Examples

if (requireNamespace("org.Hs.eg.db", quietly = TRUE) &&
    requireNamespace("reactome.db", quietly = TRUE) &&
    requireNamespace("fgsea", quietly = TRUE) &&
    requireNamespace("AnnotationDbi", quietly = TRUE)) {
    runGSEA(pbmcPlot)
}