geno.table {qtl}R Documentation

Create table of genotype distributions

Description

Create table showing the observed numbers of individuals with each genotype at each marker, including P-values from chi-square tests for Mendelian segregation.

Usage

geno.table(cross, chr)

Arguments

cross An object of class cross. See read.cross for details.
chr A vector specifying which chromosomes to consider. This may be a logical vector, a numeric vector, or a vector of character strings.

Details

The P-values are obtained from chi-square tests of Mendelian segregation. In the case of the X chromosome, the sexes and cross directions are tested separately, and the chi-square statistics combined, and so the test is of whether any of the groups show deviation from Mendel's rules.

Value

A matrix containing, for each marker, the number of individuals with each possible genotype, as well as the number that were not typed. The first column gives the chromosome ID, and the last column gives P-values from chi-square tests of Mendelian segregation.

Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

See Also

summary.cross, drop.markers, drop.nullmarkers

Examples

data(listeria)
geno.table(listeria)

geno.table(listeria, chr=13)

gt <- geno.table(listeria)
gt[gt$P.value < 0.01,]

[Package qtl version 1.07-12 Index]