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Last data update: 2014.03.03

R: Merge linkage groups of an R/qtl cross object

mergeCross

R Documentation

Merge linkage groups of an R/qtl cross object

Description

Merges linkage groups of an R/qtl cross object from a user specified list.

Usage

mergeCross(cross, merge = NULL, gap = 5)

Arguments

`cross`	An R/qtl `cross` object with any class structure.
`merge`	A list with elements containing the linkage groups to be merged with each element named by the proposed linkage group name (see Examples).
`gap`	The cM gap to put between the merged map elements in the complete linkage group.

Details

This merging function allows you to perform multiple merges of two or more linkage groups in one call. Users should ensure linkage group names are correct and that proposed linkage group names do not already exist.

Value

The cross object is returned with identical class structure as the inputted cross object. The "geno" element should now contain merged linkage groups for the user defined merges.

Author(s)

Julian Taylor

Examples


data(mapDH, package = "ASMap")

mapDH1 <- breakCross(mapDH, split = list("4A" = "4A.m.8"))
pull.map(mapDH1)[["4A.1"]]
pull.map(mapDH1)[["4A.2"]]

mapDH2 <- mergeCross(mapDH1, merge = list("4A" = c("4A.1","4A.2")))
pull.map(mapDH2)[["4A"]]

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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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/mergeCross.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mergeCross
> ### Title: Merge linkage groups of an R/qtl cross object
> ### Aliases: mergeCross
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(mapDH, package = "ASMap")
> 
> mapDH1 <- breakCross(mapDH, split = list("4A" = "4A.m.8"))
> pull.map(mapDH1)[["4A.1"]]
  4A.m.1   4A.m.2   4A.m.3   4A.m.4   4A.m.5   4A.m.6   4A.m.7   4A.m.8 
0.000000 1.332938 3.741521 3.888260 4.347020 4.805749 5.264338 5.264338 
attr(,"class")
[1] "A"
> pull.map(mapDH1)[["4A.2"]]
   4A.m.9   4A.m.10   4A.m.11   4A.m.12   4A.m.13   4A.m.14   4A.m.15   4A.m.16 
  0.00000  42.20439  44.48952  45.40706  45.86495  53.72875  56.02354  56.47843 
  4A.m.17   4A.m.18   4A.m.19   4A.m.20   4A.m.21   4A.m.22   4A.m.23   4A.m.24 
 86.78735  87.24234  88.54099  92.13963  93.05693  93.51557  94.43315  95.35073 
  4A.m.25   4A.m.26   4A.m.27   4A.m.28   4A.m.29   4A.m.30 
 95.80932  97.16742 113.28140 121.60672 133.27424 140.18485 
attr(,"class")
[1] "A"
> 
> mapDH2 <- mergeCross(mapDH1, merge = list("4A" = c("4A.1","4A.2")))
> pull.map(mapDH2)[["4A"]]
    4A.m.1     4A.m.2     4A.m.3     4A.m.4     4A.m.5     4A.m.6     4A.m.7 
  0.000000   1.332938   3.741521   3.888260   4.347020   4.805749   5.264338 
    4A.m.8     4A.m.9    4A.m.10    4A.m.11    4A.m.12    4A.m.13    4A.m.14 
  5.264338  10.264338  52.468731  54.753861  55.671402  56.129289  63.993089 
   4A.m.15    4A.m.16    4A.m.17    4A.m.18    4A.m.19    4A.m.20    4A.m.21 
 66.287874  66.742765  97.051684  97.506678  98.805332 102.403964 103.321269 
   4A.m.22    4A.m.23    4A.m.24    4A.m.25    4A.m.26    4A.m.27    4A.m.28 
103.779905 104.697487 105.615069 106.073660 107.431763 123.545740 131.871060 
   4A.m.29    4A.m.30 
143.538582 150.449188 
attr(,"class")
[1] "A"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>