pullCross {ASMap}R Documentation

Pull markers from a linkage map.

Description

Pull markers of a certain type from a linkage map and place them aside in the R/qtl object and, if appropriate, keeping their connections with the reduced linkage map.

Usage

pullCross(object, chr, type = c("co.located","seg.distortion",
          "missing"), pars = NULL, replace = FALSE, ...)

Arguments

object

An qtl cross object with class structure "bc" "dh", "riself", "bcsft". (see ?mstmap.cross for more details.)

chr

A character vector of linkage group names with which to subset the linkage map before pulling any markers.

type

A character string determining the type of markers to be pulled from the map (see Details).

pars

A list of parameters that are used by pullCross to pull markers of certain type. The default NULL calls the parameter initialization function pp.init with defaults (see Details and Examples).

replace

A logical value determining whether the markers and summary of marker information that is pulled from the map replaces information that is already residing in the type element of the object.

...

Currently ignored.

Details

This function gives users the ability to "pull" markers of several different types from the linkage map and place them in appropriately named elements of the cross object. These elements can be examined by the user and can even be "pushed" back using the complementary command pushCross.

Currently supported types are:

Value

The cross object is returned with identical class structure as the inputted cross object and an additional elements corresponding to the marker types being pulled from the map.

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

pushCross

Examples


data(mapDH, package = "ASMap")

## pull co-located markers from linkage map

mapDH.c <- pullCross(mapDH, type = "co.located")
mapDH.c$co.located$table

## pull distorted markers from linkage map using seg.thresh

mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars =
           list(seg.thresh = 0.05))
mapDH.s$seg.distortion$table

## pull distorted markers from linkage map using seg.ratio

mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars =
            list(seg.ratio = "56:44"))
mapDH.s$seg.distortion$table


[Package ASMap version 1.0-4 Index]