mhtplot {ENmix} | R Documentation

## P value manhattan plot

### 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")

[Package ENmix version 1.28.8 Index]