mhtplot: P value manhattan plot

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

Description

P value manhattan plot

Usage

        mhtplot(probe=NULL,chr=NULL, pos=NULL, p=NULL,color="bg",sigthre=NULL,
     sigthre2=NULL,threlty=c(2,1),markprobe=NULL,markcolor="red", outf="mht",
     outfmt="jpg",reducesize=0)

Arguments

probe	probe name
chr	Chromosome, 1,2,...,22,X,Y
pos	Chromosome positions
p	P values
color	Color scheme of manhattan plot, "bg" indicate "black and gray"
sigthre	P value of significant threshold line
sigthre2	P value of second significant threshold line
threlty	Threshold line type, default is c(2,1)
markprobe	A list of CpGs to be marked out
markcolor	Color code for marked probe, "red" in default
outf	figure file name, default "mht"
outfmt	Output figure file format, "jpg" or "eps"
reducesize	A positive interger, larger the value, smaller the eps file size. Smaller file size is achieved by skipping some densely packed data points

Author(s)

Zongli Xu

Examples

dat=simubed()

thre1=1E-100
dat$fdr=p.adjust(mrgd$P, method="BH")
if(sum(dat$fdr<0.05)>0){thre1=max(dat$p[dat$fdr<0.05])}

thre2=1E-7

mprobe=dat$probe[dat$p<=thre1]
mhtplot(probe=dat$probe,chr=dat$chr,pos=dat$start,p=dat$p,sigthre=thre1,sigthre2=thre2,
        markprobe=mprobe,outf="mht_try",outfmt="jpg")

ENmix documentation built on April 2, 2021, 6 p.m.