expectedGenotypes: Construct expected genotypes/haplotypes according to known...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/expectedGenotypes.R

Description

expectedGenotypes constructs expected genotypes according to known allele variants, which can be quite tedious with large number of allele variants. It can handle different level of ploidy.

Usage

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Arguments

x

genotype or haplotype

alleles

character, vector of allele names

ploidy

numeric, number of chromosome sets i.e. 2 for human autosomal genes

sort

logical, sort genotypes according to order of alleles in alleles argument

haplotype

logical, construct haplotypes i.e. ordered genotype

At least one of x or alleles must be given.

Details

expectedHaplotypes() just calls expectedGenotypes() with argument haplotype=TRUE.

Value

A character vector with genotype names as "alele1/alele2" for diploid example. Length of output is (n*(n+1))/2 for genotype (unordered genotype) and n*n for haplotype (ordered genotype) for n allele variants.

Author(s)

Gregor Gorjanc

See Also

allele.names, genotype

Examples

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  ## On genotype
  prp <- c("ARQ/ARQ", "ARQ/ARQ", "ARR/ARQ", "AHQ/ARQ", "ARQ/ARQ")
  alleles <- c("ARR", "AHQ", "ARH", "ARQ", "VRR", "VRQ")
  expectedGenotypes(as.genotype(prp))
  expectedGenotypes(as.genotype(prp, alleles=alleles))
  expectedGenotypes(as.genotype(prp, alleles=alleles, reorder="yes"))

  ## Only allele names
  expectedGenotypes(alleles=alleles)
  expectedGenotypes(alleles=alleles, ploidy=4)

  ## Haplotype
  expectedHaplotypes(alleles=alleles)
  expectedHaplotypes(alleles=alleles, ploidy=4)[1:20]

Example output

Loading required package: combinat

Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn

Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata: 
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata: 
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm


NOTE: THIS PACKAGE IS NOW OBSOLETE.



  The R-Genetics project has developed an set of enhanced genetics

  packages to replace 'genetics'. Please visit the project homepage

  at http://rgenetics.org for informtion.




Attaching package: 'genetics'

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

    %in%, as.factor, order

[1] "ARQ/ARQ" "ARQ/ARR" "ARQ/AHQ" "ARR/ARR" "ARR/AHQ" "AHQ/AHQ"
 [1] "ARQ/ARQ" "ARQ/ARR" "ARQ/AHQ" "ARQ/ARH" "ARQ/VRR" "ARQ/VRQ" "ARR/ARR"
 [8] "ARR/AHQ" "ARR/ARH" "ARR/VRR" "ARR/VRQ" "AHQ/AHQ" "AHQ/ARH" "AHQ/VRR"
[15] "AHQ/VRQ" "ARH/ARH" "ARH/VRR" "ARH/VRQ" "VRR/VRR" "VRR/VRQ" "VRQ/VRQ"
 [1] "ARR/ARR" "ARR/AHQ" "ARR/ARH" "ARR/ARQ" "ARR/VRR" "ARR/VRQ" "AHQ/AHQ"
 [8] "AHQ/ARH" "AHQ/ARQ" "AHQ/VRR" "AHQ/VRQ" "ARH/ARH" "ARH/ARQ" "ARH/VRR"
[15] "ARH/VRQ" "ARQ/ARQ" "ARQ/VRR" "ARQ/VRQ" "VRR/VRR" "VRR/VRQ" "VRQ/VRQ"
 [1] "ARR/ARR" "ARR/AHQ" "ARR/ARH" "ARR/ARQ" "ARR/VRR" "ARR/VRQ" "AHQ/AHQ"
 [8] "AHQ/ARH" "AHQ/ARQ" "AHQ/VRR" "AHQ/VRQ" "ARH/ARH" "ARH/ARQ" "ARH/VRR"
[15] "ARH/VRQ" "ARQ/ARQ" "ARQ/VRR" "ARQ/VRQ" "VRR/VRR" "VRR/VRQ" "VRQ/VRQ"
  [1] "ARR/ARR/ARR/ARR" "ARR/ARR/ARR/AHQ" "ARR/ARR/ARR/ARH" "ARR/ARR/ARR/ARQ"
  [5] "ARR/ARR/ARR/VRR" "ARR/ARR/ARR/VRQ" "ARR/ARR/AHQ/AHQ" "ARR/ARR/AHQ/ARH"
  [9] "ARR/ARR/AHQ/ARQ" "ARR/ARR/AHQ/VRR" "ARR/ARR/AHQ/VRQ" "ARR/ARR/ARH/ARH"
 [13] "ARR/ARR/ARH/ARQ" "ARR/ARR/ARH/VRR" "ARR/ARR/ARH/VRQ" "ARR/ARR/ARQ/ARQ"
 [17] "ARR/ARR/ARQ/VRR" "ARR/ARR/ARQ/VRQ" "ARR/ARR/VRR/VRR" "ARR/ARR/VRR/VRQ"
 [21] "ARR/ARR/VRQ/VRQ" "ARR/AHQ/AHQ/AHQ" "ARR/AHQ/AHQ/ARH" "ARR/AHQ/AHQ/ARQ"
 [25] "ARR/AHQ/AHQ/VRR" "ARR/AHQ/AHQ/VRQ" "ARR/AHQ/ARH/ARH" "ARR/AHQ/ARH/ARQ"
 [29] "ARR/AHQ/ARH/VRR" "ARR/AHQ/ARH/VRQ" "ARR/AHQ/ARQ/ARQ" "ARR/AHQ/ARQ/VRR"
 [33] "ARR/AHQ/ARQ/VRQ" "ARR/AHQ/VRR/VRR" "ARR/AHQ/VRR/VRQ" "ARR/AHQ/VRQ/VRQ"
 [37] "ARR/ARH/ARH/ARH" "ARR/ARH/ARH/ARQ" "ARR/ARH/ARH/VRR" "ARR/ARH/ARH/VRQ"
 [41] "ARR/ARH/ARQ/ARQ" "ARR/ARH/ARQ/VRR" "ARR/ARH/ARQ/VRQ" "ARR/ARH/VRR/VRR"
 [45] "ARR/ARH/VRR/VRQ" "ARR/ARH/VRQ/VRQ" "ARR/ARQ/ARQ/ARQ" "ARR/ARQ/ARQ/VRR"
 [49] "ARR/ARQ/ARQ/VRQ" "ARR/ARQ/VRR/VRR" "ARR/ARQ/VRR/VRQ" "ARR/ARQ/VRQ/VRQ"
 [53] "ARR/VRR/VRR/VRR" "ARR/VRR/VRR/VRQ" "ARR/VRR/VRQ/VRQ" "ARR/VRQ/VRQ/VRQ"
 [57] "AHQ/AHQ/AHQ/AHQ" "AHQ/AHQ/AHQ/ARH" "AHQ/AHQ/AHQ/ARQ" "AHQ/AHQ/AHQ/VRR"
 [61] "AHQ/AHQ/AHQ/VRQ" "AHQ/AHQ/ARH/ARH" "AHQ/AHQ/ARH/ARQ" "AHQ/AHQ/ARH/VRR"
 [65] "AHQ/AHQ/ARH/VRQ" "AHQ/AHQ/ARQ/ARQ" "AHQ/AHQ/ARQ/VRR" "AHQ/AHQ/ARQ/VRQ"
 [69] "AHQ/AHQ/VRR/VRR" "AHQ/AHQ/VRR/VRQ" "AHQ/AHQ/VRQ/VRQ" "AHQ/ARH/ARH/ARH"
 [73] "AHQ/ARH/ARH/ARQ" "AHQ/ARH/ARH/VRR" "AHQ/ARH/ARH/VRQ" "AHQ/ARH/ARQ/ARQ"
 [77] "AHQ/ARH/ARQ/VRR" "AHQ/ARH/ARQ/VRQ" "AHQ/ARH/VRR/VRR" "AHQ/ARH/VRR/VRQ"
 [81] "AHQ/ARH/VRQ/VRQ" "AHQ/ARQ/ARQ/ARQ" "AHQ/ARQ/ARQ/VRR" "AHQ/ARQ/ARQ/VRQ"
 [85] "AHQ/ARQ/VRR/VRR" "AHQ/ARQ/VRR/VRQ" "AHQ/ARQ/VRQ/VRQ" "AHQ/VRR/VRR/VRR"
 [89] "AHQ/VRR/VRR/VRQ" "AHQ/VRR/VRQ/VRQ" "AHQ/VRQ/VRQ/VRQ" "ARH/ARH/ARH/ARH"
 [93] "ARH/ARH/ARH/ARQ" "ARH/ARH/ARH/VRR" "ARH/ARH/ARH/VRQ" "ARH/ARH/ARQ/ARQ"
 [97] "ARH/ARH/ARQ/VRR" "ARH/ARH/ARQ/VRQ" "ARH/ARH/VRR/VRR" "ARH/ARH/VRR/VRQ"
[101] "ARH/ARH/VRQ/VRQ" "ARH/ARQ/ARQ/ARQ" "ARH/ARQ/ARQ/VRR" "ARH/ARQ/ARQ/VRQ"
[105] "ARH/ARQ/VRR/VRR" "ARH/ARQ/VRR/VRQ" "ARH/ARQ/VRQ/VRQ" "ARH/VRR/VRR/VRR"
[109] "ARH/VRR/VRR/VRQ" "ARH/VRR/VRQ/VRQ" "ARH/VRQ/VRQ/VRQ" "ARQ/ARQ/ARQ/ARQ"
[113] "ARQ/ARQ/ARQ/VRR" "ARQ/ARQ/ARQ/VRQ" "ARQ/ARQ/VRR/VRR" "ARQ/ARQ/VRR/VRQ"
[117] "ARQ/ARQ/VRQ/VRQ" "ARQ/VRR/VRR/VRR" "ARQ/VRR/VRR/VRQ" "ARQ/VRR/VRQ/VRQ"
[121] "ARQ/VRQ/VRQ/VRQ" "VRR/VRR/VRR/VRR" "VRR/VRR/VRR/VRQ" "VRR/VRR/VRQ/VRQ"
[125] "VRR/VRQ/VRQ/VRQ" "VRQ/VRQ/VRQ/VRQ"
 [1] "ARR/ARR" "ARR/AHQ" "ARR/ARH" "ARR/ARQ" "ARR/VRR" "ARR/VRQ" "AHQ/ARR"
 [8] "AHQ/AHQ" "AHQ/ARH" "AHQ/ARQ" "AHQ/VRR" "AHQ/VRQ" "ARH/ARR" "ARH/AHQ"
[15] "ARH/ARH" "ARH/ARQ" "ARH/VRR" "ARH/VRQ" "ARQ/ARR" "ARQ/AHQ" "ARQ/ARH"
[22] "ARQ/ARQ" "ARQ/VRR" "ARQ/VRQ" "VRR/ARR" "VRR/AHQ" "VRR/ARH" "VRR/ARQ"
[29] "VRR/VRR" "VRR/VRQ" "VRQ/ARR" "VRQ/AHQ" "VRQ/ARH" "VRQ/ARQ" "VRQ/VRR"
[36] "VRQ/VRQ"
 [1] "ARR/ARR/ARR/ARR" "ARR/ARR/ARR/AHQ" "ARR/ARR/ARR/ARH" "ARR/ARR/ARR/ARQ"
 [5] "ARR/ARR/ARR/VRR" "ARR/ARR/ARR/VRQ" "ARR/ARR/AHQ/ARR" "ARR/ARR/AHQ/AHQ"
 [9] "ARR/ARR/AHQ/ARH" "ARR/ARR/AHQ/ARQ" "ARR/ARR/AHQ/VRR" "ARR/ARR/AHQ/VRQ"
[13] "ARR/ARR/ARH/ARR" "ARR/ARR/ARH/AHQ" "ARR/ARR/ARH/ARH" "ARR/ARR/ARH/ARQ"
[17] "ARR/ARR/ARH/VRR" "ARR/ARR/ARH/VRQ" "ARR/ARR/ARQ/ARR" "ARR/ARR/ARQ/AHQ"

genetics documentation built on March 1, 2021, 9:06 a.m.