qtl (version 1.70)

top.errorlod: 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)

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.

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.

Author

Karl W Broman,

See Also

calc.errorlod, plotGeno, plotErrorlod

Examples

data(hyper)
hyper <- subset(hyper, chr=c(1,19))
# Calculate error LOD scores
hyper <- calc.errorlod(hyper,error.prob=0.01)

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