plot.genoprobs {DOQTL} | R Documentation

## 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")

[Package DOQTL version 1.16.2 Index]