Returns a list of pathways from various file formats.

This function supports custom pathway annotations to use for fedup pathway enrichment analysis. Current file formats supported are gmt, txt, and xlsx.

readPathways(
    pathwayFile,
    header = FALSE,
    pathCol = NULL,
    geneCol = NULL,
    minGene = 1L,
    maxGene = Inf
)

Arguments

pathwayFile	(char) path to file with pathway annotations
header	(logical) whether pathwayFile has a header (default FALSE)
pathCol	(char or int) column name or number with pathway identifiers (for use with non-GMT input files (eg "Pathway.ID" or 2; default NULL))
geneCol	(char or int) column name or number with gene identifiers (for use with non-GMT input files (eg "Gene.ID" or 5; default NULL))
minGene	(integer) minimum number of genes to be considered in a pathway (default 1)
maxGene	(integer) maximum number of genes to be considered in a pathway (default Inf)

Value

A list of vectors with pathway annotations.

Examples

# Generate pathway list from GMT annotation file
pathways <- readPathways(
    system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
        package = "fedup"
    ),
    minGene = 10, maxGene = 500
)
#> Pathway file: Human_Reactome_November_17_2020_symbol.gmt
#>  => n total pathways: 2418
#>  => n pathways (10-500): 1437
# Generate pathway list from XLSX annotation file
pathways <- readPathways(
    system.file("extdata", "SAFE_terms.xlsx", package = "fedup"),
    header = TRUE, pathCol = "Enriched.GO.names", geneCol = "Gene.ID"
)
#> Pathway file: SAFE_terms.xlsx
#>  => n total pathways: 317
#>  => n pathways (1-Inf): 317