ipdmr: Differentially methylated regions

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

Differentially methylated regions

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=0.05,region_plot=TRUE,mht_plot=TRUE,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
include.all.sig.sites	Whether to use CpG singletons in calculation of FDR
dist.cutoff	Maximum distance in base pair to combine adjacent DMRs, and the maximum distance between CpGs where auto-correlation will be calculated
bin.size	bin size for autocorrelation calculation
seed	FDR threshold for initial selection of DMR regions
region_plot	If TRUE, regional plots will be produced for each DMR
mht_plot	If TRUE, a p-value mahattan plot with marked DMRs will be produced
verbose	Whether to output detailed information

Details

The input should be a data frame with column names "chr","start", "end","p" and "probe", indicating chromosome, start and 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, Bioinfomatics 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.
ipdmr(data=dat,seed=0.1) #seed=0.1

xuz1/ENmix documentation built on Aug. 5, 2023, 7:11 a.m.