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

In gkeele/miqtl: Suite of QTL Mapping Functions

Plot whole genome and single chromosome windows of haplotype-based genome scan in a PDF output document

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",
  alpha = 0.05
)

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.
alpha	DEFAULT: 0.05. The specified alpha level of the positional confidence interval.

Examples

single.chr.plotter.w.ci()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.