fill.geno {qtl}R Documentation

Fill holes in genotype data

Description

Replace the genotype data for a cross with a version imputed either by simulation with sim.geno or by the Viterbi algorithm with argmax.geno.

Usage

fill.geno(cross, method=c("imp","argmax"), 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 or using the Viterbi algorithm, as implemented in argmax.geno.
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.

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.

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.

Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

See Also

sim.geno, argmax.geno

Examples

data(hyper)

out.mr <- scantwo(fill.geno(hyper,method="argmax"), method="mr")
plot(out.mr)
[Package qtl version 1.11-12 Index]