freqbinplot: Plot of unstandardized iHS within frequency bins

In rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

Description

Plot of unstandardized iHS within frequency bins.

Usage

freqbinplot(
  x,
  spectrum = FALSE,
  main = NA,
  xlab = "Derived allele frequency",
  ylab = NA,
  xlim = c(0, 1),
  ylim = NULL,
  pch = 20,
  ...
)

Arguments

x	data (output of function ihh2ihs)
spectrum	logical. If TRUE, plot frequency spectrum instead of iHS.
main	an overall title for the plot.
xlab	a title for the x axis.
ylab	a title for the y axis.
xlim	the x coordinate range of the plot.
ylim	the y coordinate range of the plot.
pch	plotting 'character' see points.
...	further arguments to be passed to plot resp. points.

Details

The plot shows the mean and the quantiles calculated by function ihh2ihs for the unstandardized iHS in each frequency bin. Note that the standardization of iHS is performed bin-wise in order to reduce the frequency-dependence of iHS values (expected under neutrality). An implicit assumption of this procedure is that each bin is dominated by neutral markers.

See Also

ihh2ihs

Examples

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

rehh documentation built on Sept. 15, 2021, 5:06 p.m.