write.founder.genomes {DOQTL} | R Documentation

## Write out the genotypes of DO samples

### 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)

[Package DOQTL version 1.16.2 Index]