summarize.genotype.transitions {DOQTL} | R Documentation

## Summarize the genotype data output by the genotyping HMM.

### Description

These functions read in all of the individual genotype data files and summarizes the founder allele frequency by sample and SNP.

### Usage

      summarize.genotype.transitions(path = ".", snps)
      summarize.by.snps(path = ".", snps)
      summarize.by.samples(path = ".", snps)
      num.recomb.plot(results, gen)

### Arguments

`path` | Character, full path to the genotype directory where the *.genotype.probs.Rdata files are stored.
`snps` | Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.
`results` | Data.frame containing results as summarized by summarize.genotype.transitions.
`gen` | Numeric vector containing DO outbreeding generation for all samples in results. Must have sample IDs in names.

### Value

Data.frame with six columns: sample, proximal genotype, distal genotype, chr, proximal Mb, distal Mb.

### Author(s)

Daniel Gatti

### Examples

      ## Not run:  geno.sum = summarize.genotype.transitions()

[Package DOQTL version 1.19.0 Index]