R: List genotypes with large error LOD scores

top.errorlod {qtl} | R Documentation

## List genotypes with large error LOD scores

### Description

Prints those genotypes with error LOD scores above a specified cutoff.

### Usage

    top.errorlod(cross, chr, cutoff=4, msg=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.
`cutoff` | Only those genotypes with error LOD scores above this cutoff will be listed.
`msg` | If TRUE, print a message if there are no apparent errors.

### Value

A data.frame with 4 columns, whose rows correspond to the genotypes that are possibly in error. The four columns give the chromosome number, individual number, marker name, and error LOD score.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`calc.errorlod`, `plotGeno`, `plotErrorlod`

### Examples

    data(hyper)

    # Calculate error LOD scores
    hyper <- calc.errorlod(hyper,error.prob=0.01)

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

[Package qtl version 1.41-6 Index]