convert.allele.calls


    Character matrix containing A, C, G, T, H or N.
  

geno


  Converts allele calls in A,C,G,T,H,N format into numbers with 0: homozygous A, 1: heterozygous, 2: homozygous B, 3: no call.


 alleles 

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

convert.allele.calls function

Character matrix containing A, C, G, T, H or N.

Converts allele calls in A,C,G,T,H,N format into numbers with 0: homozygous A, 1: heterozygous, 2: homozygous B, 3: no call.

convert.allele.calls: Convert allele calls to numeric values.

Description

Usage

Arguments

Value

Examples