GGtools-package	GGtools-package
add878	All.cis
addgwhit	All.cis
All.cis	All.cis
All.cis.eQTLs	best.cis.eQTLs
allSigCis-class	best.cis.eQTLs
appraise	appraise
b1	b1
b2	b1
batchsize	TransConfig-class
batchsize,TransConfig-method	TransConfig-class
batchsize<-	TransConfig-class
batchsize<-,TransConfig,integer-method	TransConfig-class
best.cis.eQTLs	best.cis.eQTLs
best.trans.eQTLs	best.trans.eQTLs
binnedQQ	qqhex
binqq	qqhex
buildConfList	CisConfig-class
calfig	calfig
cgff2dt	cgff2dt
chrFilter	All.cis
chrnames	CisConfig-class
chrnames,CisConfig-method	CisConfig-class
chrnames<-	CisConfig-class
chrnames<-,CisConfig,character-method	CisConfig-class
chromsUsed	best.cis.eQTLs
chromsUsed,mcwBestCis-method	best.cis.eQTLs
cis.FDR.filter.best	collectBest
cis.FDR.filter.SNPcentric	collectBest
cis.FDR.filter.SNPcentric.complete	collectBest
cisAssoc	All.cis
CisConfig-class	CisConfig-class
ciseqByCluster	ciseqByCluster
cisRun-class	cisRun-class
cisScores	All.cis
collectBest	collectBest
collectFiltered	collectBest
concatCis	concatCis
eqsens_dt	eqsens_dt
eqtlEstimates	eqtlTests
eqtlEstimatesManager-class	eqtlTestsManager-class
eqtlTests	eqtlTests
eqtlTests.me	eqtlTests.me
eqtlTestsManager-class	eqtlTestsManager-class
estimates	CisConfig-class
estimates,CisConfig-method	CisConfig-class
estimates<-	CisConfig-class
estimates<-,CisConfig,logical-method	CisConfig-class
ex	ex
excludeRadius	CisConfig-class
excludeRadius,CisConfig-method	CisConfig-class
excludeRadius<-	CisConfig-class
excludeRadius<-,CisConfig,integer-method	CisConfig-class
excludeRadius<-,CisConfig,integerOrNULL-method	CisConfig-class
exFilter	CisConfig-class
exFilter,CisConfig-method	CisConfig-class
exFilter<-	CisConfig-class
exFilter<-,CisConfig,function-method	CisConfig-class
extraProps	CisConfig-class
extraProps,CisConfig-method	CisConfig-class
extraProps<-	CisConfig-class
extraProps<-,CisConfig,function-method	CisConfig-class
fdr	best.cis.eQTLs
filtgen.maf.dist	eqsens_dt
folderStem	CisConfig-class
folderStem,CisConfig-method	CisConfig-class
folderStem<-	CisConfig-class
folderStem<-,CisConfig,character-method	CisConfig-class
fullreport	best.cis.eQTLs
fullreport,mcwBestCis,character-method	best.cis.eQTLs
fullreport,mcwBestCis,missing-method	best.cis.eQTLs
gbufsize	TransConfig-class
gbufsize,TransConfig-method	TransConfig-class
gbufsize<-	TransConfig-class
gbufsize<-,TransConfig,integer-method	TransConfig-class
gchrpref	CisConfig-class
gchrpref,CisConfig-method	CisConfig-class
gchrpref<-	CisConfig-class
gchrpref<-,CisConfig,character-method	CisConfig-class
geneannopk	CisConfig-class
geneannopk,CisConfig-method	CisConfig-class
geneannopk<-	CisConfig-class
geneannopk<-,CisConfig,character-method	CisConfig-class
geneApply	CisConfig-class
geneApply,CisConfig-method	CisConfig-class
geneApply<-	CisConfig-class
geneApply<-,CisConfig,function-method	CisConfig-class
geneIndcol	transManager-class
geneNames	transManager-class
genome	CisConfig-class
genome,CisConfig-method	CisConfig-class
genome<-	CisConfig-class
genome<-,CisConfig,character-method	CisConfig-class
genome<-,CisConfig-method	CisConfig-class
getAll	best.cis.eQTLs
getBest	best.cis.eQTLs
getCall	best.cis.eQTLs
getCisMap	getCisMap
gffprocess	gffprocess
GGtools	GGtools-package
gwSnpScreenResult-class	gwSnpTests
gwSnpTests	gwSnpTests
gwSnpTests,formula,smlSet,missing-method	gwSnpTests
gwSnpTests,formula,smlSet-method	gwSnpTests
hg19.si.df	GGtools-package
hmm878	hmm878
inflammFilter	All.cis
initialize	CisConfig-class
initialize,CisConfig-method	CisConfig-class
keepMapCache	CisConfig-class
keepMapCache,CisConfig-method	CisConfig-class
keepMapCache<-	CisConfig-class
keepMapCache<-,CisConfig,logical-method	CisConfig-class
locusNames	transManager-class
mcwAllCis-class	All.cis
mcwBestCis-class	best.cis.eQTLs
meqtlTests	eqtlTests
meta.All.cis.eQTLs	best.cis.eQTLs
meta.best.cis.eQTLs	best.cis.eQTLs
meta.bindmaf	bindmaf
meta.richNull	richNull
meta.transScores	transScores
mtransScores	transScores
nperm	CisConfig-class
nperm,CisConfig-method	CisConfig-class
nperm<-	CisConfig-class
nperm<-,CisConfig,integer-method	CisConfig-class
nthScores	transManager-class
pifdr	pifdr
plot,gwSnpScreenResult,character-method	gwSnpTests
plotsens	eqsens_dt
probesManaged	eqtlTestsManager-class
qqhex	qqhex
radius	CisConfig-class
radius,CisConfig-method	CisConfig-class
radius<-	CisConfig-class
radius<-,CisConfig,integer-method	CisConfig-class
rhs	CisConfig-class
rhs,CisConfig-method	CisConfig-class
rhs<-	CisConfig-class
rhs<-,CisConfig,formula-method	CisConfig-class
rhs<-,CisConfig,function-method	CisConfig-class
richNull	richNull
sampsInVCF	sampsInVCF
schrpref	CisConfig-class
schrpref,CisConfig-method	CisConfig-class
schrpref<-	CisConfig-class
schrpref<-,CisConfig,character-method	CisConfig-class
scoresCis	scoresCis
sensanal	sensanal
sensanal,sensiCisInput,numeric-method	sensiCisInput-class
sensiCisInput-class	sensiCisInput-class
sensiCisOutput-class	sensiCisOutput-class
shortfac	CisConfig-class
shortfac,CisConfig-method	CisConfig-class
shortfac<-	CisConfig-class
shortfac<-,CisConfig,integer-method	CisConfig-class
show	CisConfig-class
show,allCigCis-method	best.cis.eQTLs
show,allSigCis-method	best.cis.eQTLs
show,CisConfig-method	CisConfig-class
show,cisMap-method	getCisMap
show,cwBestCis-method	best.cis.eQTLs
show,eqtlTestsManager-method	eqtlTestsManager-class
show,gwSnpScreenResult,character-method	gwSnpTests
show,gwSnpScreenResult-method	gwSnpTests
show,mcwAllCis-method	All.cis
show,mcwBestCis-method	best.cis.eQTLs
show,metaVCF-method	vcf2sm
show,sensiCisInput-method	sensiCisInput-class
show,sensiCisOutput-method	sensiCisOutput-class
show,TransConfig-method	TransConfig-class
show,transManager-method	transManager-class
simpleTiling	simpleTiling
smchrpref	CisConfig-class
smchrpref,CisConfig-method	CisConfig-class
smchrpref<-	CisConfig-class
smchrpref<-,CisConfig,character-method	CisConfig-class
smFilter	CisConfig-class
smFilter,CisConfig-method	CisConfig-class
smFilter<-	CisConfig-class
smFilter<-,CisConfig,function-method	CisConfig-class
smpack	CisConfig-class
smpack,CisConfig-method	CisConfig-class
smpack<-	CisConfig-class
smpack<-,CisConfig,character-method	CisConfig-class
snpannopk	CisConfig-class
snpannopk,CisConfig-method	CisConfig-class
snpannopk<-	CisConfig-class
snpannopk<-,CisConfig,character-method	CisConfig-class
snpchr	TransConfig-class
snpchr,TransConfig-method	TransConfig-class
snpchr<-	TransConfig-class
snpchr<-,TransConfig,character-method	TransConfig-class
snplocsDefault	snplocsDefault
snpsManaged	eqtlTestsManager-class
SSgen	CisConfig-class
SSgen,CisConfig-method	CisConfig-class
SSgen<-	CisConfig-class
SSgen<-,CisConfig,function-method	CisConfig-class
strMultPop	strMultPop
TabixFile	sampsInVCF
topFeats	eqtlTestsManager-class
topFeats,probeId,eqtlTestsManager-method	eqtlTestsManager-class
topFeats,rsid,eqtlTestsManager-method	eqtlTestsManager-class
topGenes	transManager-class
topScores	transManager-class
topSnps	gwSnpTests
topSnps,gwSnpScreenResult-method	gwSnpTests
tr1_obs	transScores
tr1_perm	transScores
TransConfig-class	TransConfig-class
transeqByChrom	transeqByCluster
transeqByCluster	transeqByCluster
transManager-class	transManager-class
transScores	transScores
transScores.legacy	transScores
transTab	transTab
transTab,transManager,character-method	transTab
transTab,transManager,missing-method	transTab
update_fdr_filt	eqsens_dt
vcf2sm	vcf2sm
vcf2sm,TabixFile,GRanges,integer-method	vcf2sm
[,eqtlTestsManager,ANY,ANY,ANY-method	eqtlTestsManager-class
