do.states


  The 36 unphased genotype states for the DO on the autosomes and X chromosome. Also the 8 DO founder letter codes.


datasets

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

do.states function

A list frame with 3 elements.
  <dl>
    <dt><code>auto</code></dt><dd>Character vector with two letter codes for each of the possible DO genotype states.</dd> <dt><code>X</code></dt><dd>List with two elements, FALSE and M, containing the genotype codes for the X chromosome.</dd> <dt><code>founders</code></dt><dd>Character vector containing the founder letter codes.</dd> </dl> 

Format

The 36 unphased genotype states for the DO on the autosomes and X chromosome. Also the 8 DO founder letter codes.

do.states: do.states

Description

Usage

Arguments

Format

Details

Examples