combp: Identification of differentially methylated regions

View source: R/DMR_finding.R

combpR 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,verbose=TRUE)

Arguments

data

A data frame with colname name "chr","start", "end","p" and "probe", indicating chromosome (1,2,3,...,X,Y), chromosome start and end position, P value and probe names

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

If TRUE, regional plots will be generated

mht_plot

If TRUE, mahattan plot will be generated

nCores

Number of computer cores will be used in calculation

verbose

If TRUE, detailed running information will be printed

Details

The input should be a data frame with column names "chr","start", "end","p", and "probe", indicating chromosome number, start position, end position, P value and probe name. The function 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, Bioinformatics 2020

Examples


dat=simubed()
names(dat)
#seed=0.1 is only for demonstration purpose, it should be smaller than 0.05 or 0.01 in actual study.
combp(data=dat,seed=0.1)


xuz1/ENmix documentation built on Nov. 24, 2024, 4:31 a.m.