readPathways {fedup} | R Documentation

## Returns a list of pathways from various file formats.

### Description

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

### Usage

    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
    )
    # 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"
    )

[Package fedup version 1.2.0 Index]