GenomeAdapt (version 1.0.0)

plotmanhattan: Making manhattan plot

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

# NOT RUN {
### 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
# }
# NOT RUN {
 Hapmapqval=zscores_qvals(HapmapScan)

## plot
plotmanhattan(Hapmapqval$pvals$pvals$p.values,col=Hapmapqval$chr)
# }
# NOT RUN {
# }