ssGSEA {CrossICC} | R Documentation |
To get GSEA-like ranked matrix from CrossICC result.
ssGSEA(x, gene.signature, geneset2gene, cluster)
x |
a eSet object or eSet-like matrix. |
gene.signature |
gene signatures calculated by CrossICC. |
geneset2gene |
a matrix contains geneset (cluster name) mapping to gene. |
cluster |
CrossICC returned clusters. Note: Must mapping to x! |
a matrix with samples' eigenvalue in different super clusters.
data("demo.platforms") CrossICC.object <- CrossICC(demo.platforms, skip.mfs = TRUE, max.iter = 1, overwrite = TRUE, output.dir = tempdir()) Mcluster <- paste("K", CrossICC.object$clusters$clusters[[1]], sep = "") CrossICC.ssGSEA <- ssGSEA(x = demo.platforms[[1]], gene.signature = CrossICC.object$gene.signature, geneset2gene = CrossICC.object$unioned.genesets, cluster = Mcluster)