genome.summary.plots: Genome summary plots

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

Genome summary plots

Description

These plots show summaries of the founder haplotype proportions across SNPs or samples.

Usage

  genotype.by.sample.barplot(results)
  genotype.by.snp.barplot(results, snps)

Arguments

results	Data.frame as produced by summarize.by.snps or summarize.by.samples.
snps	Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.

Details

Barplots across samples or SNPs are produced from the relevant summary files. This is intended to be run after DO genomes have been reconstructed for a large set of samples to verify that founder allele frequencies are consistent across SNPs and samples.

Author(s)

Daniel Gatti

See Also

summarize.by.snps, summarize.by.samples

Examples

  ## Not run:  
    load(url("ftp://ftp.jax.org/MUGA/muga_snps.Rdata"))
    results = summarize.by.samples(path = ".", snps = muga_snps)
    genotype.by.sample.barplot(results) 
  
## End(Not run)

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