man/readPathways.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/pathways.R
 \name{readPathways}
 \alias{readPathways}
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 \title{Returns a list of pathways from various file formats.}
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 \usage{
 readPathways(
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     pathwayFile,
     header = FALSE,
     pathCol = NULL,
     geneCol = NULL,
     minGene = 1L,
     maxGene = Inf
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 )
 }
 \arguments{
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 \item{pathwayFile}{(char) path to file with pathway annotations}
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 \item{header}{(logical) whether \code{pathwayFile} has a header
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 (default FALSE)}
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 \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))}
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 \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))}
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 \item{minGene}{(integer) minimum number of genes to be considered
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 in a pathway (default 1)}
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 \item{maxGene}{(integer) maximum number of genes to be considered
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 in a pathway (default Inf)}
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 }
 \value{
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 A list of vectors with pathway annotations.
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 }
 \description{
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 This function supports custom pathway annotations to use
 for fedup pathway enrichment analysis. Current file formats supported are
 gmt, txt, and xlsx.
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 }
 \examples{
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 # Generate pathway list from GMT annotation file
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 pathways <- readPathways(
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     system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
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         package = "fedup"
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     ),
     minGene = 10, maxGene = 500
 )
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 # Generate pathway list from XLSX annotation file
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 pathways <- readPathways(
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     system.file("extdata", "SAFE_terms.xlsx", package = "fedup"),
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     header = TRUE, pathCol = "Enriched.GO.names", geneCol = "Gene.ID"
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 )
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 }