geneSetsFromFile {MIGSA} | R Documentation |
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.
geneSetsFromFile(filePath, ...) ## S4 method for signature 'character' geneSetsFromFile(filePath, is_GO = FALSE)
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. |
A GeneSetCollection object.
## 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)