ipdmr {ENmix} | R Documentation

## Differentially methylated region finder using interval P values

### Description

Identifing differentially methylated regions using interval P value method

### Usage

           ipdmr(data,include.all.sig.sites=TRUE,dist.cutoff=1000,bin.size=50,
                 seed=0.01,region_plot=TRUE,mht_plot=TRUE)

### Arguments

`data` | A data frame from bed format file with colname name "V1","V2", "V3","V4","V5", V1 indicate chromosome (1,2,3,...,X,Y), V2 is chromosome position, V4 is for P value and V5 for name of CpGs
`include.all.sig.sites` | Whether to use CpG singletons in calculate of FDR
`dist.cutoff` | Maximum distance in base pair to combine adjacent DMRs
`bin.size` | bin size for autocorrelation calculation
`seed` | FDR significance threshold for initial selection of DMR regions
`region_plot` | Whether to draw regional plot
`mht_plot` | Whether to draw mahattan plot

### Details

The input should be a data frame with column number V1-V5, indicate chromosome, start position, end position, P values and probe names. The function will used a novel interval p value to identify differentially methylated regions. DMR results will be output to a file with name "resu_ipdmr.csv". If plot options were selected, two figure files will be generated: mht.jpg and region_plot.pdf.

### Author(s)

Liang Niu, Zongli Xu

[Package ENmix version 1.22.6 Index]