ihsplot: Plot iHS over a genome

In theboocock/rehh: Searching for footprints of selection using Haplotype Homozygosity based tests

Description

Plot iHS over a genome.

Usage

ihsplot(data,plot.pval="TRUE",ylim.scan=2,pch=16,main="iHS")

Arguments

data	A matrix with nsnps rows and 4 columns (Chromosome name, position of the SNP, iHS, Pvalue) (e.g. obtained using ihh2ihs function.
plot.pval	Either TRUE or FALSE if Pvalue should not be plotted
ylim.scan	An horizontal line is added at the corresponding coordinate, for instance to represent a significance threshold
pch	Type of the points representing SNPs in the plot(s)
main	Main Legend of the plot

Value

The function returns a plot

References

Gautier, M. and Naves, M. (2011). Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Molecular Ecology, 20, 3128–3143.

See Also

calc_ehh,scan_hh,distribplot,ihsplot

Examples

data(wgscan.cgu) 
## results from a genome scan (44,057 SNPs)
##see ?wgscan.eut and ?wgscan.cgu for details
res.ihs<-ihh2ihs(wgscan.cgu)
ihsplot(res.ihs$res.ihs)

theboocock/rehh documentation built on May 31, 2019, 9:11 a.m.