example.pheno

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

example.pheno function

A data frame with 149 observations on the following 8 variables. Sample IDs in rownames and phenotype names in colnames.
  <dl>
    <dt><code>Sample</code></dt><dd>
	  Character vector containing sample IDs.
	</dd> <dt><code>Sex</code></dt><dd>
	  Character vector containing the sex of each animal.
	</dd> <dt><code>Gen</code></dt><dd>
	   Character vector containing DO outbreeding generation and litter.
	</dd> <dt><code>Diet</code></dt><dd>
	  Character vector containing diet, either chow or hf for high fat.
	</dd> <dt><code>Coat.Color</code></dt><dd>
	  Character vector containing text description of mouse colors.
	</dd> <dt><code>albino</code></dt><dd>
	  Numeric vector contining 1 if the mouse's coat color was white.
	</dd> <dt><code>black</code></dt><dd>
	  Numeric vector contining 1 if the mouse's coat color was black.
	</dd> <dt><code>HDLD2</code></dt><dd>
	  Numeric vector of high density lipoprotein values. 
	</dd> </dl> 

example.pheno: Example phenotypes.

Description

Usage

Arguments

Format

Details

References

Examples