alleleCount	alleleCount
alleleCount,geneSet-method	geneSet-class
alleleLevels	alleleLevels
alleleLevels,geneSet-method	geneSet-class
alleles	alleles
alleles,geneSet-method	geneSet-class
alleleSummary	alleleSummary
ALZH	ALZH
Armitage	Armitage
Armitage.default	Armitage
ArmitageTest	Armitage
as.geneSet	as.geneSet
as.geneSet.data.frame	as.geneSet
as.geneSet.matrix	as.geneSet
binsearch	binsearch
callCodes	callCodes
callCodes,geneSet-method	geneSet-class
callCodes<-	callCodes
callCodes<-,geneSet-method	geneSet-class
CAMP	CAMP
carrier	homozygote
carrier,geneSet-method	geneSet-class
carrier.geneSet	homozygote
ci.balance	ci.balance
convert	convert
decodeCallCodes	decodeCallCodes
description	description
description,geneSet-method	geneSet-class
description<-	description
description<-,geneSet-method	geneSet-class
desMarkers	desMarkers
diseq	diseq
diseq.ci	diseq
diseq.inner	diseq
dominant	homozygote
dominant,geneSet-method	geneSet-class
dominant.geneSet	homozygote
errorMetrics	errorMetrics
errorMetrics,geneSet-method	geneSet-class
errorMetrics<-	errorMetrics
errorMetrics<-,geneSet-method	geneSet-class
extractAlleles	extractAlleles
fastGrid	fastGrid
founderGeneSet	founderGeneSet
geneSet	geneSet-class
geneSet-class	geneSet-class
geneSet2Ped	geneSet2Ped
genotypeCoding	genotypeCoding
genotypeCoding.default	genotypeCoding
genotypeFileFormats	readGenes
genotypeLevels	genotypeLevels
genotypeLevels,geneSet-method	geneSet-class
genotypes	genotypes
genotypes,geneSet-method	geneSet-class
genotypeSummary	genotypeSummary
gregorius	gregorius
haplo.em.w	haplo.em.w
haplo.scan.w	haplo.scan.w
haplo.score.slide.w	haplo.score.slide.w
haplo.score.w	haplo.score.w
hapmapchr22	hapmapchr
head,geneSet-method	geneSet-class
head,LD-method	LD-class
head,LDband-method	LDband-class
head,LDdist-method	LDdist-class
heterozygote	homozygote
heterozygote,geneSet-method	geneSet-class
heterozygote.geneSet	homozygote
homozygote	homozygote
homozygote,geneSet-method	geneSet-class
homozygote.geneSet	homozygote
html	html
html,LD-method	LD-class
html.GeneticsBaseSummary	html
html.LD	html
html.markerSummary	html
HWE	HWE
HWE,geneSet-method	geneSet-class
HWE.chisq	HWE.chisq
HWE.exact	HWE.exact
latex	html
latex,LD-method	LD-class
latex.default	html
latex.GeneticsBaseSummary	html
latex.LD	html
latex.markerSummary	html
LD	LD
LD,geneSet-method	geneSet-class
LD-class	LD-class
LDband	LD
LDband,geneSet-method	geneSet-class
LDband-class	LDband-class
LDband.geneSet	LD
LDdist	LD
LDdist,geneSet-method	geneSet-class
LDdist-class	LDdist-class
LDdist.geneSet	LD
LDView	print.LD
left	left
left,LD-method	LD-class
left,LDband-method	LDband-class
left,LDdist-method	LDdist-class
makeMarkerInfo	makeMarkerInfo
makeTransTable	makeTransTable
makeTransTableList	makeTransTableList
markerFileFormats	readGenes
markerInfo	markerInfo
markerInfo,geneSet-method	geneSet-class
markerInfo<-	markerInfo
markerInfo<-,geneSet-method	geneSet-class
markerNames	markerNames
markerNames,geneSet-method	geneSet-class
markerSummary	markerSummary
missingCodes	missingCodes
missingCodes,geneSet-method	geneSet-class
missingCodes<-	missingCodes
missingCodes<-,geneSet-method	geneSet-class
nallele	nallele
nallele,geneSet-method	geneSet-class
nmarker	nmarker
nmarker,geneSet-method	geneSet-class
nobs,geneSet-method	geneSet-class
notes	notes
notes,geneSet-method	geneSet-class
notes<-	notes
notes<-,geneSet-method	geneSet-class
ped2geneSet	ped2geneSet
PerlegenExample	PerlgenExample
PfizerExample	PfizerExample
PGtables	PGtables
phase	phase
phase,geneSet-method	geneSet-class
phase<-	phase
phase<-,geneSet-method	geneSet-class
phenotypeFileFormats	readGenes
ploidy	ploidy
ploidy,geneSet-method	geneSet-class
ploidy<-	ploidy
ploidy<-,geneSet-method	geneSet-class
plot	print.LD
plot,LD-method	LD-class
plot.LD	print.LD
print.GeneticsBaseSummary	html
print.markerSummary	markerSummary
qtlex	qtlex
read.fbat.phe	read.phe
read.pbat.phe	read.phe
read.pfizer	read.pfizer
read.pfizer.Listing	read.pfizer
read.pfizer.Pivot	read.pfizer
read.phe	read.phe
readGenes	readGenes
readGenes.fbat.ped	readGenes.ped
readGenes.hapmap.ped	readGenes.ped
readGenes.pbat.ped	readGenes.ped
readGenes.ped	readGenes.ped
readGenes.perlegen	readGenes.perlegen
readGenes.pfizer	readGenes.pfizer
recessive	homozygote
recessive,geneSet-method	geneSet-class
recessive.geneSet	homozygote
right	left
right,LD-method	LD-class
right,LDband-method	LDband-class
right,LDdist-method	LDdist-class
sampleInfo	sampleInfo
sampleInfo,geneSet-method	geneSet-class
sampleInfo<-	sampleInfo
sampleInfo<-,geneSet-method	geneSet-class
show,geneSet-method	geneSet-class
show,LD-method	LD-class
show,LDband-method	LDband-class
show,LDdist-method	LDdist-class
studyInfo	studyInfo
studyInfo,geneSet-method	geneSet-class
studyInfo<-	studyInfo
studyInfo<-,geneSet-method	geneSet-class
summary.LD	LD
tail,geneSet-method	geneSet-class
tail,LD-method	LD-class
tail,LDband-method	LDband-class
tail,LDdist-method	LDdist-class
transTables	transTables
transTables,geneSet-method	geneSet-class
transTables<-	transTables
transTables<-,geneSet-method	geneSet-class
txt	html
txt.default	html
txt.GeneticsBaseSummary	html
txt.LD	html
txt.markerSummary	html
xbat	xbat
[,geneSet-method	geneSet-class
[[,geneSet-method	geneSet-class
