promoterMeth {ELMER} | R Documentation

## 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(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)

[Package ELMER version 2.12.0 Index]