promoterMeth: promoterMeth to calculate associations of gene expression...

In lijingya/ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

promoterMeth is a function to calculate associations of gene expression with DNA methylation at promoter regions.

Usage

promoterMeth(mee, sig.pvalue = 0.01, percentage = 0.2, save = TRUE)

Arguments

mee	A MEE.data object must contains four components: meth, exp, probeInfo, geneInfo.
sig.pvalue	A number specifies significant cutoff for gene silenced by promoter methylation. Default is 0.01. P value is raw P value without adjustment.
percentage	A number ranges from 0 to 1 specifying the percentage of samples of control and experimental groups used to link promoter DNA methylation to genes. Default is 0.2.
save	A logic. If it is true, the result will be saved.

Value

A data frame contains genes whose expression significantly anti-correlated with promoter methylation.

Author(s)

Lijing Yao (maintainer: [e-mail])

References

Yao L, Shen H, Laird PW, Farnham PJ,Berman BP: Inferring Regulatory Element Landscapes and Transcription Factor Networks from Cancer Methylomes. in revision of Genome Biology

Examples

load(system.file("extdata","mee.example.rda",package = "ELMER"))
Gene.promoter <- promoterMeth(mee) 

lijingya/ELMER documentation built on May 21, 2019, 6:14 a.m.