% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/pathways.R
 \name{readPathways}
 \alias{readPathways}

 \title{Returns a list of pathways from various file formats.}

 \usage{
 readPathways(

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

 )
 }
 \arguments{

 \item{pathwayFile}{(char) path to file with pathway annotations}

 \item{header}{(logical) whether \code{pathwayFile} has a header

 (default FALSE)}

 \item{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))}

 \item{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))}

 \item{minGene}{(integer) minimum number of genes to be considered

 in a pathway (default 1)}

 \item{maxGene}{(integer) maximum number of genes to be considered

 in a pathway (default Inf)}

 }
 \value{

 A list of vectors with pathway annotations.

 }
 \description{

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

 }
 \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"

 )

 }