geneRegroup: geneRegroup function

In sunny-zq/INGRID: InGRiD: Semi-supervised Identification of Cancer Subgroups using Survival Outcomes and Overlapping Grouping Information

Description

redefining the gene set membership of common genes. First, the gene remains to be as a member if it is a core member of the pathway. Second, if the gene is not a core member of any among the pathways (i.e., it maps to more than one pathways), then this gene is re-assigned to one of the gene sets based on the k-medoids algorithm minimizing the binary distance between genes within cluster distance.

Usage

geneRegroup(plist = TCGA$pathList)

Arguments

plist

user provided gene lists organized in pathways

Examples

data(TCGA)
geneRegroup.result=geneRegroup(plist=TCGA$pathList )
prefilter.results=prefilter( data=TCGA$geneexpr, time=TCGA$t, status=TCGA$d,
                             plist=geneRegroup.result@gset )

sunny-zq/INGRID documentation built on Oct. 15, 2019, 6:45 p.m.