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: 
load(srdta)
export.impute(srdta[1:50,1:3])

## End(Not run)

[Package GenABEL version 1.6-7 Index]