write.founder.genomes {DOQTL} | R Documentation |
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(filenames = dir(path = ".", pattern = "genotype.probs.Rdata"), snps) write.founder.genomes.from.haps(probs, snps)
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. |
For each sample, we take the genotype state with the highest probability and write it out.
No value is returned. FALSEiles are written to the current working directory.
Daniel Gatti
## Not run: write.founder.genomes(filenames = dir(path = ".", pattern = "genotype.probs.Rdata")) ## End(Not run)