Delete genotypes that are possibly in error
Delete genotypes from a cross that are indicated to be possibly in error, as they result in apparent tight double-crossovers.
cleanGeno(cross, chr, maxdist=2.5, maxmark=2, verbose=TRUE)
cross |
An object of class |
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 |
maxdist |
A vector specifying the maximum distance between two crossovers. |
maxmark |
A vector specifying the maximum number of typed markers between two crossovers. |
verbose |
If TRUE, print information on the numbers of genotypes omitted from each chromosome. |
We first use locateXO to identify crossover locations.
If a pair of adjacted crossovers are separated by no more than
maxdist and contain no more than maxmark genotyped
markers, the intervening genotypes are omitted (that is, changed to
NA).
The arguments maxdist and maxmark may be vectors. (If
both have length greater than 1, they must have the same length.) If
they are vectors, genotypes are omitted if they satisify any one of
the (maxdist, maxmark) pairs.
The input cross object with suspect genotypes omitted.
Karl W Broman, broman@wisc.edu
data(hyper) sum(ntyped(hyper)) hyperc <- cleanGeno(hyper, chr=4, maxdist=c(2.5, 10), maxmark=c(2, 1)) sum(ntyped(hyperc))
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