mhtplot {ENmix} | R Documentation |
P value manhattan plot
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)
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 |
Zongli Xu
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")