typingGap: Maximum distance between genotyped markers

In qtl: Tools for Analyzing QTL Experiments

Maximum distance between genotyped markers

Description

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

Usage

typingGap(cross, chr, terminal=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.
terminal	If TRUE, just look at terminal typing gaps (from the terminal markers to the first typed marker).

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.) If terminal=TRUE, we look only at those beginning and end distances.

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.)

Author(s)

Karl W Broman, [e-mail]

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]]))))

plot(typingGap(hyper, chr=4),
     ylab="Maximum gap between typed markers (cM)",
     ylim=c(0, diff(range(pull.map(hyper,chr=4)[[1]]))))

plot(typingGap(hyper, chr=4, terminal=TRUE),
     ylab="Maximum gap between chr end and typed marker (cM)",
     ylim=c(0, diff(range(pull.map(hyper,chr=4)[[1]]))))

qtl documentation built on Nov. 28, 2023, 1:09 a.m.