summarize.genotype.transitions

summarize.by.samples

summarize.by.snps

num.recomb.plot


    Character, full path to the genotype directory where the *.genotype.probs.Rdata files are stored.
  

path


     Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.
  

snps


    Data.frame containing results as summarized by summarize.genotype.transitions.
  

results


    Numeric vector containing DO outbreeding generation for all samples in results. Must have sample IDs in names.
  


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


 HMM 

 genotyping 

 Diversity Outbred 

DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.

Daniel Gatti

DOQTL

Genotyping and QTL Mapping in DO Mice

summarize.genotype.transitions function

Character, full path to the genotype directory where the *.genotype.probs.Rdata files are stored.

Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.

Data.frame containing results as summarized by summarize.genotype.transitions.

Numeric vector containing DO outbreeding generation for all samples in results. Must have sample IDs in names.

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

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

Description

Usage

Arguments

Value

Examples