geno.table {qtl}

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, scanone.output=FALSE)

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.

scanone.output

If TRUE, give result in the form output by scanone, so that one may use plot.scanone, etc.

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

If scanone.output=FALSE, the output is 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.

If scanone.output=TRUE, the output is of the form produced by scanone, with the first two columns being chromosome IDs and cM positions of the markers. The third column is -\log_{10}(P) from chi-square tests of Mendelian segregation. The fourth column is the proportion of missing data. The remaining columns are the proportions of the different genotypes (among typed individuals).

Author(s)

Karl W Broman, [e-mail]

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,]

out <- geno.table(listeria, scanone.output=TRUE)
plot(out)
plot(out, lod=2)