promoterMeth: promoterMeth to calculate associations of gene expression with DNA methylation
at promoter regions.
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.
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