combp {ENmix}R Documentation

Identification of differentially methylated regions

Description

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

References

Pedersen BS1, Schwartz DA, Yang IV, Kechris KJ. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinfomatics 2012

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]