qtl (version 1.21-2)

typingGap: Maximum distance between genotyped markers

Description

Calculates, for each individual on each chromosome, the maximum distance between genotyped markers.

Usage

typingGap(cross, chr)

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 c

Value

• A matrix with rows corresponding to individuals and columns corresponding to chromosomes. (If there is just one chromosome, it is a numeric vector rather than a matrix.)

Details

We consider not just the distances between internal genotypes, but also distances from the beginning of the chromosome to the first typed marker, and similarly for the end of the chromosome. (The start and end of a chromosome are taken to be the locations of the initial and final markers.)

See Also

ntyped, nmissing, locateXO

Examples

data(hyper)
plot(typingGap(hyper, chr=5), ylab="Maximum gap between typed markers (cM)",
     ylim=c(0, diff(range(pull.map(hyper,chr=5)[[1]]))))