GenABEL (version 1.8-0)

convert.snp.mach: function to convert genotypic data from MACH format to internal data format

Description

Converts genotypic data from MACH format to internal genotypic data formated file (NOT recommended)

Usage

convert.snp.mach(pedfile, mapfile, infofile, outfile, quality = 0.9, 
					column.quality = 7, strand = "+", ...)

Arguments

pedfile

File with genotypic data from MACH (geno or mlgeno)

mapfile

Name of the map file (note that header line should be included)

infofile

Name MACH info-file

outfile

Output data file

quality

Drop the SNPs with quality (as specified in some column of info-file) lower than this threshold.

column.quality

What column of the info-file provides "quality". Default = 7 os r2; possible values include 6 (average postrior probability).

strand

Specification of strand, one of "u" (unknown), "+", "-" or "file". In the latter case, map-file should contain an extended map (the one including strand and coding). See options to convert.snp.ped for details.

...

Other arguments passed to convert.snp.ped

Value

Does not return any value, but writes file with GenABEL raw data

Details

This is a simple script converting the MACH data with convert.snp.ped, re-loading data, and filtering the snp.data object based on quality as specified in MACH info-file Note that it is NOT recommended to process imputations results with this procedure, as uncertainty inherent to imputations is lost after processing ("hard" calls are made)! For the purposes of GWA analysis, we recommend procedures, which make direct use of estimated allele dose or genotypic probabilities.

See Also

load.gwaa.data, convert.snp.illumina, convert.snp.text, convert.snp.ped, convert.snp.tped

Examples

#
# convert.snp.mach(ped="pedin.18",map="map.18",out="genos.raw")
#