GenABEL (version 1.8-0)

export.impute: 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

Value

No value returned; all infor stored in files

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)

See Also

export.merlin.

Examples

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