Read GSEA Results from TSV Files — read_gsea_tsv • deseq2pip

This function reads GSEA results from TSV files for multiple comparisons and collections.

Usage

read_gsea_tsv(
  group_dir = getwd(),
  collection = c("HALLMARK", "GOBP", "KEGG", "REACTOME", "BIOCARTA", "TFT"),
  merge = T
)

Arguments

group_dir: Parent directory containing comparison subdirectories. Default is current working directory
collection: Vector of gene set collections to load. Default includes HALLMARK, GOBP, KEGG, REACTOME, BIOCARTA, and TFT
merge: Logical. If TRUE, returns a single merged data frame. If FALSE, returns a list of data frames

Value

Either a merged data frame or a list of data frames containing GSEA results

Examples

if (FALSE) { # \dontrun{
# Read and merge all results
merged_gsea <- read_gsea_tsv("results", merge = TRUE)

# Read specific collections as a list
gsea_list <- read_gsea_tsv("results", collection = c("HALLMARK", "KEGG"), merge = FALSE)
} # }