plot.genoprobs {DOQTL} | R Documentation |
This function plots the genotype of a DO sample by taking the genotype with the maximum probability at each marker.
## 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)
x |
Numeric matrix containing the 36 genotype state probabilities generated by |
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. |
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.
Daniel Gatti
## Not run: plot.genoprobs(prsmth, snps, main = "plot title")