| geno.table {qtl} | R Documentation |
Create table showing the observed numbers of individuals with each genotype at each marker, including P-values from chi-square tests for Mendelian segregation.
geno.table(cross, chr)
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. |
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.
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.
Karl W Broman, kbroman@biostat.wisc.edu
summary.cross,
drop.markers, drop.nullmarkers
data(listeria) geno.table(listeria) geno.table(listeria, chr=13) gt <- geno.table(listeria) gt[gt$P.value < 0.01,]