find.errors {qtl}R Documentation

Identify likely genotyping errors

Description

Compares the observed genotypes to the most likely sequence of underlying genotypes given the observed marker data (calculated in argmax.geno), to identify genotypes likely to be in error.

Usage

find.errors(cross, chr, error.prob=0.01,
            map.function=c("haldane","kosambi","c-f"),msg=TRUE)

Arguments

cross An object of class cross. See read.cross for details.
chr A vector specifying for which chromosomes the calculations should be performed.
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.
msg If TRUE, print a message if there are no apparent errors.

Details

The most likely sequence of underlying genotypes is calculated in argmax.geno. This function simply pulls out those genotypes where the observed genotype differs from that appearing in the argmax.geno results.

Value

A matrix with 5 columns, whose rows correspond to the genotypes that are possibly in error. The five columns give the chromosome number, individual number, marker name, observed genotype and most likely genotype.

Author(s)

Karl W Broman, kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html

See Also

argmax.geno, plot.errors

Examples

data(fake.f2)
output <- find.errors(fake.f2)
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