Break linkage groups of an qtl cross object

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.

References

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

Author

Julian Taylor

Examples


data(mapDH, package = "ASMap")

mapDH1 <- breakCross(mapDH, split = list("4A" = "4A.m.8"))
pull.map(mapDH1)[["4A.1"]]
#>   4A.m.1   4A.m.2   4A.m.3   4A.m.4   4A.m.5   4A.m.6   4A.m.7   4A.m.8 
#> 0.000000 1.332938 3.741521 3.888260 4.347020 4.805749 5.264338 5.264338 
#> attr(,"class")
#> [1] "A"
pull.map(mapDH1)[["4A.2"]]
#>    4A.m.9   4A.m.10   4A.m.11   4A.m.12   4A.m.13   4A.m.14   4A.m.15   4A.m.16 
#>   0.00000  42.20439  44.48952  45.40706  45.86495  53.72875  56.02354  56.47843 
#>   4A.m.17   4A.m.18   4A.m.19   4A.m.20   4A.m.21   4A.m.22   4A.m.23   4A.m.24 
#>  86.78735  87.24234  88.54099  92.13963  93.05693  93.51557  94.43315  95.35073 
#>   4A.m.25   4A.m.26   4A.m.27   4A.m.28   4A.m.29   4A.m.30 
#>  95.80932  97.16742 113.28140 121.60672 133.27424 140.18485 
#> attr(,"class")
#> [1] "A"

## manually choose suffix

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