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]