typingGap {qtl} | R Documentation |
Calculates, for each individual on each chromosome, the maximum distance between genotyped markers.
typingGap(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. |
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.)
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.)
Karl W Broman, kbroman@biostat.wisc.edu
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]]))))