as.genotype.gwaa.data: Attempts to convert gwaa.data to "genotype"

In GenABEL: genome-wide SNP association analysis

Description

A function to convert @gtdata slot of an object of gwaa.data-class to "genotype" data frame

Usage

	## S3 method for class 'gwaa.data'
as.genotype(x, ...)

Arguments

x	An object of gwaa.data-class
...	...

Value

A data-frame containing genotypes consumable by "genetics" library

Author(s)

Yurii Aulchenko

See Also

as.character.gwaa.data, as.character.snp.data, as.double.gwaa.data, as.double.snp.data, as.hsgeno, as.genotype.gwaa.data, as.genotype.snp.data

Examples

require(GenABEL.data)
data(srdta)
as.genotype(srdta[1:5,1:10])

Example output

Loading required package: MASS
Loading required package: GenABEL.data
Loading required package: genetics
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: 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 object is masked from 'package:GenABEL':

    as.genotype

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

    %in%, as.factor, order

   rs10 rs18 rs29 rs65 rs73 rs114 rs128 rs130 rs143 rs150
p1  T/T  G/G  G/G  T/A  A/A   A/A   G/G   A/A   G/G   A/A
p2  T/T  G/G <NA> <NA>  A/A   A/A   G/G   G/G   T/T   C/C
p3  T/T  G/G <NA>  T/A  A/A   A/A   G/G   A/A   G/G   A/A
p4  T/T  G/G <NA> <NA>  A/A   A/A   G/G   G/G  <NA>   A/C
p5  T/T  G/A  G/G  T/T  A/A   A/A   G/G   G/G   G/G   A/A

GenABEL documentation built on May 30, 2017, 3:36 a.m.