GGtools-package	GGtools-package
checkCommonSNPs	makeCommonSNPs
chunksize	gwSnpTests
chunksize-class	gwSnpTests
cisProxScores	cisProxScores
cisProxScores-class	cisProxScores-class
cisTransDirector-class	eqtlTestsManager-class
clipPCs	clipPCs
degnerASE01	degnerASE01
dropMonomorphies	dropMonomorphies
eqtlEstimates	eqtlTests
eqtlEstimatesManager-class	eqtlEstimatesManager-class
eqtlFDRtab-class	eqtlFDRtab-class
eqtlTests	eqtlTests
eqtlTestsManager-class	eqtlTestsManager-class
ex	hmceuB36.2021
ex6	ex6
exome_minp	exome_minp
externalize	externalize
geneIndcol	geneIndcol
geneNames	geneIndcol
genewiseFDRtab	genewiseFDRtab
getGene2SnpList	probeLocations
GGtools	GGtools-package
gwSnpTests	gwSnpTests
gwSnpTests,formula,smlSet,cnumOrMissing,ANY-method	gwSnpTests
gwSnpTests,formula,smlSet,cnumOrMissing,missing-method	gwSnpTests
gwSnpTests,formula,smlSet,cnumOrMissing-method	gwSnpTests
gwSnpTests,formula,smlSet,snpdepth,ANY-method	gwSnpTests
gwSnpTests,formula,smlSet,snpdepth,chunksize-method	gwSnpTests
gwSnpTests,formula,smlSet,snpdepth,missing-method	gwSnpTests
gwSnpTests,formula,smlSet,snpdepth-method	gwSnpTests
hla2set	hla2set
ieqtlTests	eqtlTests
imphm3_1KG_20_mA2	imphm2_1KG_20
imphm3_1KG_20_mA5	imphm2_1KG_20
interleave2cis	cisProxScores
locusNames	geneIndcol
m20	m20
makeCommonSNPs	makeCommonSNPs
makeDiagDirector	multiCisDirector-class
manhPlot	manhPlot
mkCisTransDirector	mkCisTransDirector
mrefhap2sm	mrefhap2sm
mtransScores	transScores
multiCisDirector-class	multiCisDirector-class
nthScores	geneIndcol
pcChooser	pcChooser
permEx	permEx
plot,cwSnpScreenResult,missing-method	plot-methods
plot,filteredGwSnpScreenResult,ANY-method	plot-methods
plot,filteredMultiGwSnpScreenResult,ANY-method	plot-methods
plot,snp.reg.imputation,missing-method	plot-methods
policywiseFDRtab	genewiseFDRtab
probeChromosomes	probeLocations
probeLocations	probeLocations
probeNames	eqtlTestsManager-class
probeNames,cisTransDirector-method	eqtlTestsManager-class
probeNames,eqtlTestsManager-method	eqtlTestsManager-class
probeSequences	probeLocations
probesManaged	eqtlTestsManager-class
probesManaged,eqtlTestsManager,numeric-method	eqtlTestsManager-class
proximityList	probeLocations
relocate	relocate
residTests	gwSnpTests
residTests,cwSnpScreenResult,smlSet,formula,missing-method	gwSnpTests
restrictProbesToChrom	probeLocations
scoresByGenes	cisProxScores
show,cisProxScores-method	cisProxScores-class
show,cisTransDirector-method	eqtlTestsManager-class
show,eqtlFDRtab-method	eqtlFDRtab-class
show,eqtlTestsManager-method	eqtlTestsManager-class
show,gwScores-method	eqtlFDRtab-class
show,metaVCF-method	vcf2sm
show,multiCisDirector-method	multiCisDirector-class
show,pwScores-method	eqtlFDRtab-class
show,transManager-method	transManager-class
sm2ped	sm2ped
snpLocations	probeLocations
snpsManaged	eqtlTestsManager-class
snpsManaged,eqtlTestsManager,numeric-method	eqtlTestsManager-class
strMultPop	strMultPop
topFeats	X2chunk
topFeats,genesym-method	X2chunk
topFeats,probeId-method	X2chunk
topFeats,rsid-method	X2chunk
topGenes	geneIndcol
topScores	geneIndcol
topSnps	topSnps-methods
topSnps,cwSnpScreenResult-method	topSnps-methods
topSnps,gwSnpScreenResult-method	topSnps-methods
topSnps-methods	topSnps-methods
tr1_obs	transScores
tr1_perm	transScores
transManager-class	transManager-class
transScores	transScores
transTab	transTab
vcf2sm	vcf2sm
vcf2sm,TabixFile,GRanges,integer-method	vcf2sm
X2chunk	X2chunk
[,cisTransDirector,character,character,ANY-method	eqtlTestsManager-class
[,cisTransDirector,character,missing,ANY-method	eqtlTestsManager-class
[,cisTransDirector,missing,character,ANY-method	eqtlTestsManager-class
[,eqtlEstimatesManager,ANY,ANY,ANY-method	eqtlEstimatesManager-class
[,eqtlTestsManager,ANY,ANY,ANY-method	eqtlTestsManager-class
[,eqtlTestsManager,missing,probeId,ANY-method	eqtlTestsManager-class
[,eqtlTestsManager,rsid,missing,ANY,ANY-method	eqtlTestsManager-class
[,eqtlTestsManager,rsid,missing,ANY-method	eqtlTestsManager-class
[,eqtlTestsManager,rsid,probeId,ANY-method	eqtlTestsManager-class
