pathwayGeneTab: Pathway-Gene Associations

In pouryany/PanomiR: Detection of miRNAs that regulate interacting groups of pathways

Pathway-Gene Associations

Description

Generates a table of pathways and genes associations.

Usage

pathwayGeneTab(
  pathAdress = NA,
  pathwayList = NA,
  fromType = "ENTREZID",
  toType = "ENSEMBL",
  outDir = NA
)

Arguments

pathAdress	Address to an RDS file containing list of pathways where each element is a list of genes similar to GMT format.
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.
fromType	gene annotation type used in your input data.
toType	gene annotation type to be produced in the output.
outDir	Address to save an RDS for a table of pathway-gene association

Value

pathExpTab Table of pathway-gene association.

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])

pouryany/PanomiR documentation built on Aug. 20, 2022, 11:17 p.m.