uniConSigPreCal-package: Calculate uniConSig scores using pre-calculated files

In wangxlab/uniConSigPreCal: Fast calculation of uniConSig and CSEA

Description

Using pre-calculated files to calculate the functional associations between a single gene and a gene set. Also implement down stream CSEA functions to facilitate pathway analysis.

Details

The package include two major functions:

cal_uniConSig(trList,preCal=preCal.data)

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

The input of uniConSig is trList, which is a vector containing the entrez gene IDs of interest. The output of cal_uniConSig can be directly put into the second function "CSEA" as the first argument. The second and the third argument specify the pathway gene set. Currently only c2cp and hallmark pathways from MSigdb are compiled.

Author(s)

Xu Chi

Maintainer: Xu Chi <[e-mail]>

References

https://github.com/wangxlab/uniConSigPreCal

Examples

#See vignettes for full calculation of uniConSig scores.
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.