selectPath-methods: pathway selection using LASSO

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

Description

LASSO step for pathway selection. To identify patient subgroups based on pathway level risk profile, we fit a LASSO-Penalized Cox regression on scores derived from all the pathways.

Usage

## S4 method for signature 'FitGene'
selectPath(object, seed = 123)

Arguments

object	results of selectGene step
seed	random seed that was set, default = 123.

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 )
gene.results=selectGene( object=prefilter.results, fold=5, K=5, etas=c(0.1,0.9),seed=123)
path.results=selectPath( object=gene.results, seed=123)

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