ssGSEA: To get GSEA-like ranked matrix from CrossICC result.

In CrossICC: An Interactive Consensus Clustering Framework for Multi-platform Data Analysis

Description

To get GSEA-like ranked matrix from CrossICC result.

Usage

ssGSEA(x, gene.signature, geneset2gene, cluster)

Arguments

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!

Value

a matrix with samples' eigenvalue in different super clusters.

Examples

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)

CrossICC documentation built on April 29, 2020, 4:40 a.m.