prefilter: prefilter function

In sunny-zq/PICS: PICS (Pathway-guided Identification of Cancer Subgroups)

Description

a supervised prefiltering by fitting a cox regression model on the expression measures of each mRNA. Only genes with p values smaller than a pre-selected cut-off point were included in further analysis. Here we chose p=0.5 as default cut-off point.

Usage

prefilter(data, time, status, p.cut = 0.5, plist = plist)

Arguments

data	A N by P dataframe, where N is number of observations, P is number of genes
time	time passed to selectGene's time argument.
status	status selectGene's status argument.
p.cut	p.cut is the pvalue cutoff point for prefiltering
plist	user provided gene lists organized in pathways

Examples

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

sunny-zq/PICS documentation built on May 30, 2019, 8:39 p.m.