qtl (version 0.92-3)

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=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.

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