genome.plots: Plot the genome of a DO sample.

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

Plot the genome of a DO sample.

Description

This function plots the genotype of a DO sample by taking the genotype with the maximum probability at each marker.

Usage

  ## S3 method for class 'genoprobs'
plot(x, snps, colors = "DO", chrlen = "mm10", ...)
  chr.skeletons(chr, chrlen, ...)
  genomic.points(chr = NULL, loc = NULL)
  write.genoprob.plots(path = ".", snps)

Arguments

x	Numeric matrix containing the 36 genotype state probabilities generated by calc.genoprob.
snps	Data.frame containing the SNP locations in prsmth. SNP ID, chromosome, Mb and cM locations in columns 1 through 4, respectively.
colors	Character string containing "DO" for the DO. FALSEor all other crosses, a data.frame containing single letter codes, strain names and colors for the founders in columns 1 through 3, respectively.
chrlen	Character string containing the genome for the chromosome lengths. Default = mm10.
genome	Character string containing the genome for the chromosome lengths. Default = mm10.
chr	Vector of chromosome IDs.
path	Character string containing the path to the posterior genotype probability files in R binary format (i.e. *.Rdata).
loc	Numeric vector of genome locations in Mb of same length as chr.
...	Additional arguments to be passed to plot.

Value

plot.genoprobs plots the reconstructed DO genome in terms of founder haplotypes. chr.skeletons plots the chromosome skeletons. This is useful for further plotting. genomic.points plots locations on a genome such as might be drawn by chr.skeletons. write.genoprob.plots loops through all of the files supplied in the argument and writes out genotype plots.

Author(s)

Daniel Gatti

See Also

calc.genoprob

Examples

  ## Not run: plot.genoprobs(prsmth, snps, main = "plot title")

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.