summarize.genotype.transitions: Summarize the genotype data output by the genotyping HMM.

In DOQTL: Genotyping and QTL Mapping in DO Mice

Description

These functions read in all of the individual genotype data files and summarizes the founder allele frequency by sample and SNP.

Usage

  summarize.genotype.transitions(path = ".", snps)
  summarize.by.snps(path = ".", snps)
  summarize.by.samples(path = ".", snps)
  num.recomb.plot(results, gen) 

Arguments

path	Character, full path to the genotype directory where the *.genotype.probs.Rdata files are stored.
snps	Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.
results	Data.frame containing results as summarized by summarize.genotype.transitions.
gen	Numeric vector containing DO outbreeding generation for all samples in results. Must have sample IDs in names.

Value

Data.frame with six columns: sample, proximal genotype, distal genotype, chr, proximal Mb, distal Mb.

Author(s)

Daniel Gatti

Examples

  ## Not run:  geno.sum = summarize.genotype.transitions() 

DOQTL documentation built on May 6, 2019, 3:09 a.m.