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.

See Also

as.Genesets

Genesets-enrichr

loadGo

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);


[Package MIGSA version 1.6.0 Index]