loadGenesets {SeqGSEA} | R Documentation |
This function is to load annotation of gene sets from files. The files are in the format of Molecular Signatures Database (MSigDB), and those files can be downloaded at http://www.broadinstitute.org/gsea/msigdb/index.jsp.
loadGenesets(geneset.file, geneIDs, geneID.type = c("gene.symbol", "ensembl"), genesetsize.min = 5, genesetsize.max = 1000, singleCell = FALSE)
geneset.file |
the file containing the gene set annotation. |
geneIDs |
gene IDs that have expression values in the studied data set. |
geneID.type |
indicating the type of gene IDs, gene symbol or emsembl gene IDs. |
genesetsize.min |
the minimum number of genes in a gene set that will be treated in the analysis. |
genesetsize.max |
the maximum number of genes in a gene set that will be treated in the analysis. |
singleCell |
logical, whether to creat a SeqGeneSet object for scGSEA. |
TBA
A SeqGeneSet object.
Xi Wang, xi.wang@newcastle.edu.au
## Not run: data(RCS_example, package="SeqGSEA") geneIDs <- geneID(RCS_example) geneID.type <- "ensembl" geneset.file <- system.file("extdata", "gs_symb.txt", package="SeqGSEA", mustWork=TRUE) GS <- loadGenesets(geneset.file, geneIDs, geneID.type = geneID.type) GS ## End(Not run)