R: Identify likely genotyping errors

calc.errorlod {qtl}

R Documentation

Identify likely genotyping errors

Description

Calculates a LOD score for each genotype, indicating which ones are likely to be in error.

Usage

calc.errorlod(cross, error.prob=0.01, map.function=c("haldane","kosambi","c-f"))

Arguments

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

Uses the function calc.genoprob to calculate conditional genotype probabilities given observed marker genotypes, and then calculates the LOD score described by Lincoln and Lander (1992) for each genotype, indicating likely errors. The actual calculations are done in the C program calc_errorlod.

An attribute "error.prob" is set to the value of the corresponding argument, for later reference.

Value

The cross object in the input is returned with a component, errorlod, added to each component of cross$geno. The errorlod component is a matrix of size (n.ind x n.mar).

Author(s)

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

References

SE Lincoln and ES Lander (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604-610

Examples

data(fake.f2)
fake.f2 <- calc.genoprob(fake.f2,error.prob=0.01)
fake.f2 <- calc.errorlod(fake.f2,error.prob=0.01)
plot.errorlod(fake.f2)

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