pushCross {ASMap}R Documentation

Push markers into an established R/qtl linkage map.

Description

Push unlinked markers or markers that were originally placed aside by pullCross back into linkage groups of an established R/qtl linkage map.

Usage

pushCross(object, type = c("co.located","seg.distortion",
          "missing","unlinked"), unlinked.chr = NULL,
          pars = NULL, ...)

Arguments

object

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

type

A character string determining the type of markers to be pushed into the linkage map (see Details).

unlinked.chr

A character string of linkage group names containing markers that require pushing into the remaining linkage groups of the object. This is only useful when type="unlinked". Default is NULL.

pars

A list of parameters that are used by pushCross to push markers a certain type back into the linkage group. The default NULL calls the parameter initialization function pp.init with defaults (see Details and Examples).

...

Currently ignored.

Details

This function was written explicitly to complement pullCross by "pushing" markers of certain types back into linkage groups of an established linkage map.

Currently supported marker types are:

For types "seg.distortion", "missing" and "unlinked" a fast clustering method is used to allocate markers to established linkage groups. This is done very efficiently by reducing the constructed linkage map to a skeleton set of markers before checking linkages. How these linkages are formed can be tweaked by setting max.rf and min.lod when calling pars. These currently default to max.rf = 0.25 and min.lod = 3.

Users should explicitly avoid the use of "UL" as part of a linkage group name as this is used internally to name unlinked groups of markers if required. It should also be noted that this function does not re-construct the object after allocating markers to linkage groups. For efficient linkage map reconstruction of an R/qtl object see mstmap.cross().

Value

The cross object is returned with an identical class structure as the inputted cross object with additional markers from the marker types pushed into linkage groups of the established linkage map. If all markers of an element type are pushed back then the element type is removed from the object.

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

pullCross

Examples


data(mapDH, package = "ASMap")

## pull co-located markers from map

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

## push co-located markers back into linkage map

mapDH.z <- pushCross(mapDH.c, type = "co.located")
pull.map(mapDH.z)


[Package ASMap version 1.0-4 Index]