pullCross: Pull markers from a linkage map.

In ASMap: Linkage Map Construction using the MSTmap Algorithm

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:

• type = "co.located". This type gives the user the ability to reduce a linkage map to a unique set of markers for the purpose of efficient map construction. Co-located markers are pulled from the linkage map using the technology of findDupMarkers from the qtl package and places them aside in a separate list element called "co.located". This element contains the removed marker data as well as a table that displays the connections between the co-located markers with markers that remain in the linkage map. If required, this table is used by pushCross to "push" the co-located markers back into the linkage map.

• type = "seg.distortion". Users can pull markers with segregation distortion from a linkage map with two different thresholding mechanisms called using pars. If the list argument pars is used with an element called seg.thresh then markers are pulled from the map if the p-value from the test for segregation distortion is LESS than seg.thresh. Values of seg.thresh must be between 0 and 1. If pars contains an element seg.ratio then markers are pulled from the map 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 pulled if their allele proportions are GREATER than the largest proportional ratio or LESS 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. If markers are found matching the above criteria they are pulled from the linkage map and placed aside in an element called "seg.distortion". This element contains the removed distorted marker data as well as a table summarizing each of the markers. See examples below for more detail.

• type = "missing". Users can pull markers with a proportional amount of missing allele scores. If pars contains an element miss.thresh then markers are pulled from the linkage map that have a proportion of missing values GREATER than miss.thresh. If no value is given for miss.thresh then it defaults to 0.1 or 10% missing values. If markers are found matching the above criteria they are pulled from the map and are placed aside in an separate list element called "missing". This element contains the removed marker data as well as a table summarizing each of the markers. See examples below for more detail.

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

ASMap documentation built on Nov. 1, 2024, 9:08 a.m.