function to convert genotypic data from MACH format to internal data format

convert.snp.mach {GenABEL}R Documentation

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

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.

Value

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

Note

The function does not check if "outfile" already exists, thus it is always over-written

Author(s)

Yurii Aulchenko

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")
#

[Package GenABEL version 1.6-7 Index]