export.merlin: function to export GenABEL data in merlin format

In GenABEL: genome-wide SNP association analysis

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, 
	     dpieceFun = "new")

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
dpieceFun	function used to dump data. Do use default.

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])
#

Example output

Loading required package: MASS
Loading required package: GenABEL.data

GenABEL documentation built on May 30, 2017, 3:36 a.m.