fill.geno: Fill holes in genotype data

Description

Replace the genotype data for a cross with a version imputed either by simulation with sim.geno, by the Viterbi algorithm with argmax.geno, or simply filling in genotypes between markers that have matching genotypes.

Usage

fill.geno(cross, method=c("imp","argmax", "no_dbl_XO"), error.prob=0.0001,
          map.function=c("haldane","kosambi","c-f","morgan"))

Arguments

cross

An object of class cross. See read.cross for details.

method

Indicates whether to impute using a single simulation replicate from sim.geno, using the Viterbi algorithm, as implemented in argmax.geno, or by s

error.prob

Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype).

map.function

Indicates whether to use the Haldane, Kosambi or Carter-Falconer map function when converting genetic distances into recombination fractions.

Value

The input cross object with the genotype data replaced by an imputed version. Any intermediate calculations (such as is produced by calc.genoprob, argmax.geno and sim.geno) are removed.

Details

This function is written so that one may perform rough genome scans by marker regression without having to drop individuals with missing genotype data. We must caution the user that little trust should be placed in the results.

With method="no_dbl_XO", there may be missing genotypes remaining (between two markers that show a recombination event, at the ends of the chromosomes, or with incompletely informative genotypes).

Examples

Run this code

data(hyper)
hyper <- subset(hyper,chr=18:19)
out.mr <- scantwo(fill.geno(hyper,method="argmax"), method="mr")
plot(out.mr)