combp {ENmix}R Documentation

Differentially methylated region finder using a modified comb-p method

Description

Identifing differentially methylated regions using a modified comb-p method

Usage

       combp(data,dist.cutoff=1000,bin.size=310,seed=0.01,
             region_plot=TRUE,mht_plot=TRUE,nCores=10)

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

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 region

region_plot

Whether to draw regional plot

mht_plot

Whether to draw mahattan plot

nCores

Number of computer cores used in calculation

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 modified comb-p method to identify differentially methylated regions. DMR results will be output to a file with name "resu_combp.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]