Combine linkage maps from multiple R/qtl cross objects

Description

Combine map information, marker data and phenotype data from multiple R/qtl cross objects

Usage

combineMap(..., id = "Genotype", keep.all = TRUE)

Arguments

Details

This function combines linkage maps from multiple R/qtl cross objects by merging marker data and map information as well as phenotypic data if present. The function contains some initial checks before proceeding with the combining. Firstly, all R/qtl cross objects must have the same class structure and have a column in the pheno element of the object named by the argument id. The marker names must also be unique across linkage maps as well as avoid the symbol ";". This symbol is reserved for string manipulation within the function.

The combining of linkage maps occurs in multiple ways. Firstly, it merges the linkage maps sequentially based on genotype names. If keep.all=TRUE then the marker data and phenotypic data are "padded out" when genotype names are not shared between maps. If keep.all=FALSE then the marker data and phenotype data are shrunk to only include genotypes that are shared among all linkage maps. Secondly, if a linkage group name is shared across linkage maps then the marker data from the shared linkage group in each of the maps will be merged.

Several things are important to note with this function. Non-matching genotype names between linkage maps will expand the final marker data and phenotypic data so it is prudent to check genotype names are correct in each of the linkage maps before combining. If maps share the same linkage group names and do not require merging the duplicate linkage group names in one of the linkage maps will need to be altered before combining. As a final process, markers are ordered within linkage groups according to distances supplied in each of the linkage maps.

It should also be noted that this function does not re-construct the final linkage map after combining the set of linkage maps. For efficient linkage map reconstruction of the combined R/qtl object see mstmap.cross().

Value

A single R/qtl cross object is returned with identical class structure as the inputted cross objects.

Author(s)

Julian Taylor

See Also

breakCross and mergeCross

Examples

data(mapDH, package = "ASMap")

## create copy of mapDH with some different linkage groups
## and change marker names so they are unique

mapDH1 <- mapDH
names(mapDH1$geno)[5:14] <- paste("L",1:10, sep = "")
mapDH1$geno <- lapply(mapDH1$geno, function(el){
    names(el$map) <- dimnames(el$data)[[2]] <- paste(names(el$map), "A", sep = "")
    el})

mapDHc <- combineMap(mapDH, mapDH1)
nmar(mapDHc)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ASMap)
Loading required package: qtl
Loading required package: gtools
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps

 # maps v3.1: updated 'world': all lakes moved to separate new #
 # 'lakes' database. Type '?world' or 'news(package="maps")'.  #


Loading required package: RColorBrewer
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ASMap/combineMap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: combineMap
> ### Title: Combine linkage maps from multiple R/qtl cross objects
> ### Aliases: combineMap
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(mapDH, package = "ASMap")
> 
> ## create copy of mapDH with some different linkage groups
> ## and change marker names so they are unique
> 
> mapDH1 <- mapDH
> names(mapDH1$geno)[5:14] <- paste("L",1:10, sep = "")
> mapDH1$geno <- lapply(mapDH1$geno, function(el){
+     names(el$map) <- dimnames(el$data)[[2]] <- paste(names(el$map), "A", sep = "")
+     el})
> 
> mapDHc <- combineMap(mapDH, mapDH1)
> nmar(mapDHc)
 1A 1B1 1B2  1D  2A  2B 2D1 2D2  3A  3B  3D  4A  4B  4D  5A  5B  5D  6A  6B  6D 
 82  10  66  20  40  35   8  13  37  30   6  30  32   6 108 112  12  54  82  30 
 7A  7B  7D  L1  L2  L3  L4  L5  L6  L7  L8  L9 L10 
 66  74   8  40  35   8  13  37  30   6  30  32   6 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>