CSEA: Calculate CSEA

In wangxlab/uniConSigPreCal: Fast calculation of uniConSig and CSEA

Description

transfer the uniConSig result to function "weightedKS_ofCSEA()"

Usage

CSEA(result.uniConSig, posList, nPermu = 1000)

Arguments

result.uniConSig	The result generated by "cal_uniConSig"
posList	A list of list containing pathways of genes. Each sublist is a pathway (or a concept), containing Entrez gene IDs
nPermu	The number of permutations. Default 1000. Note that this number should be consistent with pre-calculated permutation list.

Value

A table of 3 columns, "pathway names","NES","pValue"

Examples

##For a training list, starting from uniConSig:
trList.call<-1:100
result<-cal_uniConSig(trList.call)
pathway.my<-list()
pathway.my[[1]]<-1:10
pathway.my[[2]]<-5:15
result.csea<-CSEA(result,pathway.my)

wangxlab/uniConSigPreCal documentation built on May 23, 2019, 9:31 a.m.