pushCross {ASMap}

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:

• type = "co.located". Users can push co-located markers back into the linkage map that have been set aside in the cross object element co.located. To ensure this can be used at any stage of the linkage map construction process the function disregards the linkage group information provided in the table formed by using pullCross. Instead it uses the current positions of the markers in the reduced linkage map to determine where to push the co-located markers back to.

• type = "seg.distortion". Users can push markers from the "seg.distortion" element of the object back into a linkage map using the thresholding mechanisms seg.thresh and seg.ratio called using pars. If seg.thresh is given then the markers are pushed back that have p-values that are GREATER than seg.thresh. If pars contains an element seg.ratio then markers are pushed back based on the ratio provided. The ratio must be in character format and of the type "AA:BB" for two allele populations and "AA:AB:BB" for three allele populations (see Examples for more details). Markers are pushed back if their allele proportions are LESS than the largest proportional ratio or GREATER than the smallest proportional ratio given in seg.thresh. If neither thresholding mechanisms are given then the default is to use seg.thresh = 0.05.

• type = "missing". Users can push markers from the object element "missing" back into the linkage map using the thresholding parameter miss.thresh called using pars. Markers will be pushed back that have a proportion of missing values LESS than miss.thresh. If no value is given for this parameter it defaults to 0.1 or 10% missing values.

• type = "unlinked". Users can push unlinked markers that reside in linkage groups of the established linkage map. If this type is chosen unlinked.chr must be a character string of linkage group names in the object.

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)