breakCross {ASMap}

Break linkage groups of an qtl cross object

Description

Breaks linkage groups of an qtl cross object from a user specified list.

Usage

breakCross(cross, split = NULL, suffix = "numeric", sep = ".")

Arguments

cross

An qtl cross object with any class structure.

split

A list named by the linkage groups required for splitting and containing marker names immediately preceding where the splits are to be made (see Details).

suffix

This can be a vector of character strings containing "numeric" or "alpha" specifying whether integers or letters are to be appended to the old linkage group names to form new names. This argument may also be list with elements named by the linkage groups that are in split and containing the new names for the split linkage groups (see Examples).

sep

The character separator to be used to separate the linkage group name and the suffix.

Details

The splitting of any linkage group only needs to be defined by the markers immediately preceding where the splits are to be made. Multiple splits in the one linkage group are possible as well as splitting across multiple linkage groups with one call.

Value

The cross object is returned with identical class structure as the inputted cross object. The "geno" element will contain separate linkage groups for the user defined splits.

Author(s)

Julian Taylor

References

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.

See Also

mergeCross

Examples

data(mapDH, package = "ASMap")

mapDH1 <- breakCross(mapDH, split = list("4A" = "4A.m.8"))
pull.map(mapDH1)[["4A.1"]]
pull.map(mapDH1)[["4A.2"]]

## manually choose suffix

mapDH1 <- breakCross(mapDH, split = list("4A" = "4A.m.8"),
                     suffix = list("4A" = c("4AA","4AB")))