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, plot.geno

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 1.11-12 Index]