R: Creates a GeneSetCollection object from a file

geneSetsFromFile {MIGSA}

R Documentation

Creates a GeneSetCollection object from a file

Description

geneSetsFromFile creates a GeneSetCollection object from the data present in a file. The file must be a tab separated values file (tsv). Each line will parse to a GeneSet. First field will be the GeneSet setName, the second the setIdentifier and the remaining are the genes.

Usage

geneSetsFromFile(filePath, ...)

## S4 method for signature 'character'
geneSetsFromFile(filePath, is_GO = FALSE)

Arguments

`filePath`	character with the path of the file to parse.
`...`	not in use.
`is_GO`	logical indicating if this gene sets are from the Gene Ontology. If true, then each gene GeneSet setName must be a GO id.

Value

A GeneSetCollection object.

Examples

## Create some fake gene sets in a data.frame to save them in disk and then
## load them (10 gene sets with 20 genes each (it is not neccesary that they
## have the same number of genes).
gsets <- data.frame(
  IDs = paste("set", 1:10),
  Names = rep("", 10),
  matrix(paste("gene", 1:(10 * 20)), nrow = 10)
)
## And save this file as a tab separated file.
geneSetsFile <- paste(tempdir(), "/fakeGsets.tsv", sep = "")
write.table(gsets,
  file = geneSetsFile, sep = "\t",
  col.names = FALSE, row.names = FALSE, quote = FALSE
)
## Now lets load this tsv file as a GeneSetCollection object.
myGsets <- geneSetsFromFile(geneSetsFile)
## And lets delete this tsv file (so we dont have garbage in our disk).
unlink(geneSetsFile)