R: function to export GenABEL data in IMPUTE format

export.impute {GenABEL} | R Documentation

## function to export GenABEL data in IMPUTE format

### Description

Exports GenABEL data to IMPUTE/SNPTEST/GTOOLS format

### Usage

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

### Arguments

`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

### Details

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)

### Value

No value returned; all infor stored in files

### Author(s)

Yurii Aulchenko

### See Also

`export.merlin`.

### Examples

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

    ## End(Not run)

[Package GenABEL version 1.8-0 Index]