get.max.geno


    Three dimensional numeric matrix containing the founder haplotype contributions.
  

probs


  For each sample at each marker, return the genotype state with the highest probability.


 genotype 

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

get.max.geno function

Three dimensional numeric matrix containing the founder haplotype contributions.

For each sample at each marker, return the genotype state with the highest probability.

get.max.geno: Get the genotype with the highest probability

Description

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Examples