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

In 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(data, sig.pvalue = 0.01, minSubgroupFrac = 0.4,
             upstream = 200,  downstream = 2000, save = TRUE, cores = 1)

Arguments

data	A Multi Assay Experiment object with DNA methylation and gene expression Summarized Experiment objects
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.
minSubgroupFrac	A number ranging from 0 to 1 specifying the percentage of samples used to create the groups U (unmethylated) and M (methylated) used to link probes to genes. Default is 0.4 (lowest quintile of all samples will be in the U group and the highest quintile of all samples in the M group).
upstream	Number of bp upstream of TSS to consider as promoter region
downstream	Number of bp downstream of TSS to consider as promoter region
save	A logic. If it is true, the result will be saved.
cores	Number of cores to be used in paralellization. Default 1 (no paralellization)

Details

promoterMeth

Value

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

Examples

## Not run: 
  data(elmer.data.example.promoter)
  Gene.promoter <- promoterMeth(mae.promoter)

## End(Not run)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.