man/pathwayGeneTab.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils.R
 \name{pathwayGeneTab}
 \alias{pathwayGeneTab}
 \title{Pathway-Gene Associations}
 \usage{
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 pathwayGeneTab(
   pathAdress = NA,
   pathwayList = NA,
   fromType = "ENTREZID",
   toType = "ENSEMBL",
   outDir = NA
 )
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 }
 \arguments{
 \item{pathAdress}{Address to an RDS file containing list of pathways where
 each element is a list of genes similar to GMT format.}
 
 \item{pathwayList}{If you wish to use a list of pathways instead of a file
 use this argument instead. The list must contain no NA values.}
 
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 \item{fromType}{gene annotation type used in your input data.}
 
 \item{toType}{gene annotation type to be produced in the output.}
 
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 \item{outDir}{Address to save an RDS for a table of pathway-gene association}
 }
 \value{
 pathExpTab Table of pathway-gene association.
 }
 \description{
 Generates a table of pathways and genes associations.
 }
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 \examples{
 pathway1 <- c("125", "3099", "126")
 pathway2 <- c("5232", "5230", "5162")
 pathList <- list("Path1" = pathway1, "Path2" = pathway2)
 res <- pathwayGeneTab(pathwayList = pathList)
 
 data(msigdb_c2)
 pathwayGeneTab(pathwayList = msigdb_c2[1:2])
 }