single.chr.plotter.w.ci: Plot whole genome and single chromosome windows of...

In gkeele/kqtl: Suite of QTL Mapping Functions

Description

This function takes the genome scan output from scan.h2lmm() and plots the whole genome and single chromosome zoom-ins for all the specified chromosomes. When multiple imputations are used, includes the 95% confidence band on the median in the zoomed-in plots.

Usage

single.chr.plotter.w.ci(scan.object, qtl.ci.object, ci.type, scan.type,
  these.col = c("#7BAFD4", "red"), scale = "Mb")

Arguments

scan.object	A scan.h2lmm() object (ROP or multiple imputations). If multiple imputations, median and confidence interval on median are plotted. Expected to the scan of the actual data.
qtl.ci.object	A run.positional.scans() object. Should contain single chromosome scans from some form of sampling process, such as a parametric bootstrap.
ci.type	Positional confidence interval to be included in the title. Example: "Parametric Bootstrap".
scan.type	Scan type to be included in the title. Example: "ROP".
these.col	Colors to be used for individual artificial scans.
scale	DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either "Mb" or "cM" is expected.

Examples

single.chr.plotter.w.ci()

gkeele/kqtl documentation built on May 17, 2019, 6:06 a.m.