plotmanhattan: Making manhattan plot

In GenomeAdapt: Detecting Signatures of Local Adaptation Based on Ancestry Trajectories

Description

Ploting a Manhattan plot showing the (q)p-values for each SNP.

Usage

plotmanhattan(x, ylim=c(0,200),xlab="",
ylab="-log(p-value)",col = x$chr, pch="*",h=10, lcol="blue", ...)

Arguments

x	The zscores_qvals object
ylim	The y axis range
xlab	The x title
ylab	The y title
col	The colour used for indicating chromosomes
pch	The shape of of the data points.
h	The cutoff line
lcol	The colour of the cutoff line
...	passing to other parameters of plot

Value

Return to a manhattan plot with (q)p-values for each SNP.

Examples

### using Hapmap data
HapmapScan=GenomeAdapt.gds(genfile = SNPRelate::snpgdsExampleFileName(),
method="EIGMIX",num.thread = 1L, autosome.only=TRUE,
remove.monosnp=TRUE, maf=0.01, missing.rate=0.1)

### Not running, it takes a while to finish this
 Hapmapqval=zscores_qvals(HapmapScan)

## plot
plotmanhattan(Hapmapqval$pvals$pvals$p.values,col=Hapmapqval$chr)

GenomeAdapt documentation built on Nov. 12, 2021, 1:06 a.m.