export.impute: function to export GenABEL data in IMPUTE format
In GenABEL: genome-wide SNP association analysis

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

Exports GenABEL data to IMPUTE/SNPTEST/GTOOLS format

1 2	export.impute(data,genofile="impute.gen",samplefile="impute.sample", strandfile="impute.strand",cachesizeMb=128)

`data`	gwaa.data object
`genofile`	Output genotype data file name
`samplefile`	Output sample information file name, 'id' header line + IDs of people will be written there
`strandfile`	name for strand output file
`cachesizeMb`	approximate amount of RAM to be used to generate chunks of data

The most interesting part is the genotype file which is generated, this file contains one SNP per row, with columns

SNP_name_1 SNP_name_2 Position Allele1 Allele2 P_1_11 P_1_12 P_1_22 P_2_11 P_2_12 P_2_22 ...

where SNP_name_1 = SNP_name_2 is SNP name, Position is SNP position, Allele1 and Allele2 are reference and effective alleles; P_i_jk is the probability that person i has genotype jk; these are (1 0 0) for genotype Allele1Allele1, (0 1 0) for genotype Allele1Allele2, (0 0 1) for genotype Allele2Allele2, and (0 0 0) if genotype is missing

Strand file contains the SNP name, position and strand, as generated by as.character(data@gtdata@strand); this is up to user if this slot contains correct data (see eg convert.snp.illumina on how to import strand info)

No value returned; all infor stored in files

Yurii Aulchenko

export.merlin.

## Not run: 
require(GenABEL.data)
data(srdta)
export.impute(srdta[1:50,1:3])

## End(Not run)

Loading required package: MASS
Loading required package: GenABEL.data
writing sample file ...... done!
writing strand file ...
... done!
writing genotypes ...
[1] "writing SNPs from 1 to 3 ..."
... done!