export.merlin {GenABEL}R Documentation

function to export GenABEL data in merlin format

Description

Exports GenABEL data to Merlin and other pedigree formats

Usage

        export.merlin(data, pedfile = "merlin.ped", datafile = "merlin.dat", mapfile = "merlin.map", 
        format = "merlin", fixstrand = "no", extendedmap = TRUE, traits = 1)

Arguments

data gwaa.data object
pedfile Output pedigree data file name
datafile Output data (information) file name
mapfile Output map file name
format Output format: reserved for future use, currently only "merlin"
fixstrand "no" – the strand information and coding comes from the data; "+" – change all coding to "+" strand, "-" – change all coding to "-" strand
extendedmap if TRUE extended map (+ strand, + coding) is saved with the name "mapfile.ext", where "mapfile" is the parameter supplied by user
traits How many fake traits to insert before first column of marker data

Details

The use is straightforward, with only the "fixstrand" option requiring some explanation. Consider a SNP on "-" strand with alleles G and A. If this SNP is accessed on "+" strand, the corresponding alleles would be C and T. While for example Affymetrix reports SNPs on bot "+" and "-" strands, HapMap reports coding on "+" strand only. To make data compatible, and/or to run imputations, one will need to convert all SNP codes to "+" strand. This can be achieved by running export.merlin() with fixstrand="+" parameter.

Value

No value returned

Author(s)

Yurii Aulchenko

See Also

To load the data to GenABEL again, use convert.snp.ped, load.gwaa.data.

Examples

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

[Package GenABEL version 1.4-2 Index]