R: Delete genotypes that are possibly in error

cleanGeno {qtl} | R Documentation

## Delete genotypes that are possibly in error

### Description

Delete genotypes from a cross that are indicated to be possibly in error, as they result in apparent tight double-crossovers.

### Usage

    cleanGeno(cross, chr, maxdist=2.5, maxmark=2, verbose=TRUE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`chr` | Optional vector indicating the chromosomes to consider. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`maxdist` | A vector specifying the maximum distance between two crossovers.
`maxmark` | A vector specifying the maximum number of typed markers between two crossovers.
`verbose` | If TRUE, print information on the numbers of genotypes omitted from each chromosome.

### Details

We first use `locateXO` to identify crossover locations. If a pair of adjacted crossovers are separated by no more than `maxdist` and contain no more than `maxmark` genotyped markers, the intervening genotypes are omitted (that is, changed to `NA`).

The arguments `maxdist` and `maxmark` may be vectors. (If both have length greater than 1, they must have the same length.) If they are vectors, genotypes are omitted if they satisify any one of the (`maxdist`, `maxmark`) pairs.

### Value

The input `cross` object with suspect genotypes omitted.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`locateXO`, `countXO`, `calc.errorlod`

### Examples

    data(hyper)
    sum(ntyped(hyper))
    hyperc <- cleanGeno(hyper, chr=4, maxdist=c(2.5, 10), maxmark=c(2, 1))
    sum(ntyped(hyperc))

[Package qtl version 1.41-6 Index]