useDynLib(GenABEL)

import(methods)
import(genetics)
importClasses(genetics)

export(
	add.plot,
	as.character.gwaa.data,
	as.character.snp.coding,
	as.character.snp.data,
	as.character.snp.strand,
	as.data.frame.gwaa.data,
	as.double.gwaa.data,
	as.double.snp.data,
	as.genotype,
	as.genotype.gwaa.data,
	as.genotype.snp.data,
	as.hsgeno,
	as.hsgeno.gwaa.data,
	as.hsgeno.snp.data,
	catable,
	ccfast,
	check.marker,
	check.trait,
	convert.snp.illumina,
	convert.snp.mach,
	convert.snp.ped,
	convert.snp.tped,
	convert.snp.text,
	crnames,
	descriptives.marker,
	descriptives.scan,
	descriptives.trait,
	dprfast,
	egscore,
	emp.ccfast,
	emp.qtscore,
	estlambda,
	export.merlin,
	grammar,
	HWE.show,
	hom,
	ibs,
	load.gwaa.data,
	mmscore,
	perid.summary,
	plot.check.marker,
	plot.scan.gwaa,
	plot.scan.gwaa.2D,
	polygenic,
	r2fast,
	redundant,
	refresh.gwaa.data,
	rhofast,
	qtscore,
	qvaluebh95,
	save.gwaa.data,
	scan.glm,
	scan.glm.2D,
	scan.haplo,
	scan.haplo.2D,
	show.ncbi,
	snp.data,
	snp.names,
	snp.subset,
	sset,
	summary.check.marker,
	summary.gwaa.data,
	summary.snp.data,
	Xfix
       )

exportClasses(
	"gwaa.data",
	"scan.gwaa",
	"scan.gwaa.2D",
	"snp.coding",
	"snp.data",
	"snp.mx",
	"snp.strand",
	"snps.cell"
	)

exportMethods("show")

S3method(summary,check.marker)
S3method(summary,gwaa.data)
S3method(summary,snp.data)

S3method(plot,check.marker)
S3method(plot,scan.gwaa)
S3method(plot,scan.gwaa.2D)

S4method('[',snp.data)
S4method('[',gwaa.data)
S4method('[',snp.mx)

S3method(as.character,gwaa.data)
S3method(as.character,snp.data)
S3method(as.data.frame,gwaa.data)
S3method(as.double,snp.data)
S3method(as.double,gwaa.data)
S3method(as.hsgeno,gwaa.data)
S3method(as.hsgeno,snp.data)
S3method(as.genotype,gwaa.data)
S3method(as.genotype,snp.data)
