function to export GenABEL data in merlin format

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, order = TRUE, stepids = 100)

Arguments

data gwaa.data object
pedfile Output pedigree data file name
datafile Output data (information) file name; no output if NULL
mapfile Output map file name
format Output format, either "merlin" or "plink"
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
order Should output be ordered by chromosome and position
stepids make this larger for faster processing and smaller for lower RAM use

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; files saved on HDD

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 1.6-7 Index]