R: Identify likely genotyping errors

calc.errorlod {qtl} | R Documentation

## Identify likely genotyping errors

### Description

Calculates a LOD score for each genotype, measuring the evidence for genotyping errors.

### Usage

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

### 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, Carter-Falconer, or Morgan map function when converting genetic distances into recombination fractions.
`version` | Specifies whether to use the original version of this function or the current (preferred) version.

### Details

Calculates, for each individual at each marker, a LOD score measuring the strength of evidence for a genotyping error, as described by Lincoln and Lander (1992).

In the latest version, evidence for a genotype being in error is considered assuming that all other genotypes (for that individual, on that chromosome) are correct. The argument `version` allows one to specify whether this new version is used, or whether the original (old) version of the calculation is performed.

Note that values below 4 are generally not interesting. Also note that if markers are extremely tightly linked, recombination events can give large error LOD scores. The error LOD scores should not be trusted blindly, but should be viewed as a tool for identifying genotypes deserving further study.

Use `top.errorlod` to print all genotypes with error LOD scores above a specified threshold, `plotErrorlod` to plot the error LOD scores for specified chromosomes, and `plotGeno` to view the observed genotype data with likely errors flagged.

### Value

The input `cross` object 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). An attribute `"error.prob"` is set to the value of the corresponding argument, for later reference.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### References

Lincoln, S. E. and Lander, E. S. (1992) Systematic detection of errors in genetic linkage data. Genomics 14, 604–610.

### See Also

`plotErrorlod`, `top.errorlod`, `cleanGeno`

### Examples

    data(hyper)

    hyper <- calc.errorlod(hyper,error.prob=0.01)

    # print those above a specified cutoff
    top.errorlod(hyper, cutoff=4)

    # plot genotype data, flagging genotypes with error LOD > cutoff
    plotGeno(hyper, chr=1, ind=160:200, cutoff=7, min.sep=2)

[Package qtl version 1.41-6 Index]