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

In DOQTL: Genotyping and QTL Mapping in DO Mice

Description

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.

Usage

  write.founder.genomes(filenames = dir(path = ".", 
  pattern = "genotype.probs.Rdata"), snps)
  write.founder.genomes.from.haps(probs, snps)

Arguments

filenames	Character vector of posterior genotype probability files in R binary format.
probs	Three dimensional numeric array containing the 8 state haplotype probabilities. Dimensions samples x founders x markers.
snps	Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.

Details

For each sample, we take the genotype state with the highest probability and write it out.

Value

No value is returned. FALSEiles are written to the current working directory.

Author(s)

Daniel Gatti

Examples

  ## Not run:  write.founder.genomes(filenames = dir(path = ".", 
  pattern = "genotype.probs.Rdata")) 
## End(Not run)

DOQTL documentation built on May 6, 2019, 3:09 a.m.