combp: Identification of differentially methylated regions

In xuz1/ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

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 Aug. 5, 2023, 7:11 a.m.