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=3, 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 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@jhsph.edu

See Also

calc.errorlod, plot.errorlod

Examples

data(hyper)

# run calc.genoprob, then calc.errorlod; use same error.prob
hyper <- calc.genoprob(hyper,error.prob=0.01)
hyper <- calc.errorlod(hyper,error.prob=0.01)

# plot the error LOD scores; print those above a specified cutoff 
plot.errorlod(hyper)
plot.errorlod(hyper,chr=1)
top.errorlod(hyper,cutoff=4)

# plot genotype data, flagging genotypes with error LOD > cutoff
plot.geno(hyper, chr=1, ind=160:200, cutoff=7, min.sep=2)

# Note that if markers are extremely tightly linked,
#     any recombination event will have a high error LOD
plot.geno(hyper, chr=1, ind=101:118, min.sep=2)
hyper$geno[[1]]$map

[Package qtl version 0.98-57 Index]