write.founder.genomes

write.founder.genomes.from.haps


    Character vector of posterior genotype probability files in R binary format.
  

filenames


    Three dimensional numeric array containing the 8 state haplotype probabilities. Dimensions samples x founders x markers.
  

probs


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

snps


  Given a directory containing files generated by the DOQTL HMM (i.e. that end with "genotype.probs.Rdata"), write out two files for each sample containing the founder haplotype blocks.


 haplotypes 

 genotypes 

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

write.founder.genomes function

Character vector of posterior genotype probability files in R binary format.

Three dimensional numeric array containing the 8 state haplotype probabilities. Dimensions samples x founders x markers.

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

Given a directory containing files generated by the DOQTL HMM (i.e. that end with "genotype.probs.Rdata"), write out two files for each sample containing the founder haplotype blocks.

write.founder.genomes: Write out the genotypes of DO samples

Description

Usage

Arguments

Value

Details

Examples