Subset an R/qtl object

Subset an R/qtl object by chromosome or by individuals for populations used within the R/ASMap package.

Usage

subsetCross(cross, chr, ind, ...)

Arguments

cross: A "cross" object generated from the R/qtl package. Specifically the object needs to inherit from one of the following classes "bc", "dh", "riself", "bcsft" (see Details).
chr: Optional vector specifying which chromosomes to keep or discard. This may be a logical, numeric, or character string vector. See ?subset.cross.
ind: Optional vector specifying which individuals to keep or discard. This may be a logical or numeric vector (see Details).
...: Kept for compatability with subset.cross and is ignored at this point.

Details

This function is a replacement version of subset.cross that should be used if the cross object contains any or all of the components "co.located", "seg.distortion" and "missing" created by a pullCross call. For a given ind, the function calls subset.cross to ensure that all elements created from calls to native R/qtl functions are subsetted appropriately. In addition, the "co.located", "seg.distortion" and "missing" elements are also subsetted and if components "seg.distortion" and "missing" exist, statistics in their respective tables are recalculated.

It provides identical functionality to subset.cross with the exception that ind can only be a logical or numeric vector.

Value

The cross object is returned with the appropriate subsetting.

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")

mapDH.s <- pullCross(mapDH, type = "seg.distortion")
mapDH.s <- subsetCross(mapDH.s, ind = 3:218)
dim(mapDH.s$seg.distortion$data)
#> [1] 216  41