ipdmr {ENmix}R Documentation

Differentially methylated region finder using interval P values

Description

To identify differentially methylated regions using an 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 names V1-V5, indicating chromosome, start position, end position, P value and probe name. The function will use a novel interval p value method to identify differentially methylated regions. DMR results will be stored in 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

References

Zongli Xu, Changchun Xie, Jack A. Taylor, Liang Niu, ipDMR: Identification of differentially methyl-ated regions with interval p-values, in review


[Package ENmix version 1.25.1 Index]