top.errorlod {qtl}R Documentation

List genotypes with highest error LOD values

Description

Pulls from the output of calc.errorlod those genotypes with error LOD scores above a specified cutoff.

Usage

top.errorlod(cross, chr, cutoff=2, msg=TRUE)

Arguments

cross An object of class cross. See read.cross for details.
chr A vector specifying for which chromosomes the error LOD scores should be inspected.
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 matrix 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@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html

See Also

calc.errorlod, plot.errorlod, find.errors, plot.errors

Examples

data(fake.f2)
fake.f2 <- calc.genoprob(fake.f2)
fake.f2 <- calc.errorlod(fake.f2)
top.errorlod(fake.f2,c(5,13),3)
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