snpStats-package	snpStats-package
Asnps	testdata
Autosomes	testdata
can.impute	imputation.maf
cbind,SnpMatrix-method	SnpMatrix-class
cbind2,SnpMatrix,SnpMatrix-method	SnpMatrix-class
ceph.1mb	ld.example
chi.squared	chi.squared
chi.squared,GlmTests,missing-method	GlmTests-class
chi.squared,SingleSnpTests,numeric-method	SingleSnpTests-class
coerce,GlmEstimates,GlmTests-method	GlmEstimates-class
coerce,GlmTests,data.frame-method	GlmTests-class
coerce,matrix,SnpMatrix-method	SnpMatrix-class
coerce,SingleSnpTests,data.frame-method	SingleSnpTests-class
coerce,SnpMatrix,character-method	SnpMatrix-class
coerce,SnpMatrix,numeric-method	SnpMatrix-class
coerce,SnpMatrix,XSnpMatrix-method	XSnpMatrix-class
coerce,XSnpMatrix,character-method	XSnpMatrix-class
col.summary	row.summary
convert.snpMatrix	convert.snpMatrix
convert.snpMatrix.dir	convert.snpMatrix
deg.freedom	chi.squared
deg.freedom,GlmTests-method	GlmTests-class
effect.sign	chi.squared
effect.sign,GlmTests,logical-method	GlmTests-class
effect.sign,SingleSnpTestsScore,missing-method	SingleSnpTests-class
effective.sample.size	chi.squared
effective.sample.size,SingleSnpTests-method	SingleSnpTests-class
example-new	example-new
families	families
filter.rules	filter.rules
for.exercise	for.exercise
Fst	Fst
g2post	mean2g
genotypes	families
glm.test.control	glm.test.control
GlmEstimates-class	GlmEstimates-class
GlmTests-class	GlmTests-class
GlmTestsScore-class	GlmTests-class
ibsCount	ibsCount
ibsDist	ibsDist
imputation.maf	imputation.maf
imputation.nsnp	imputation.maf
imputation.r2	imputation.maf
ImputationRules-class	ImputationRules-class
impute.snps	impute.snps
initialize,SnpMatrix-method	SnpMatrix-class
initialize,XSnpMatrix-method	XSnpMatrix-class
is.na,SnpMatrix-method	SnpMatrix-class
ld	ld
ld.example	ld.example
mach1.out.mlprob.gz	sample
mean2g	mean2g
misinherits	misinherits
mvtests	mvtests
names,GlmTests-method	GlmTests-class
names,SingleSnpTests-method	SingleSnpTests-class
p.value	chi.squared
p.value,GlmTests,missing-method	GlmTests-class
p.value,SingleSnpTests,numeric-method	SingleSnpTests-class
pedData	families
plot,ImputationRules,missing-method	ImputationRules-class
plotUncertainty	plotUncertainty
pool	pool
pool2	pool2
pool2,GlmTestsScore,GlmTestsScore,logical-method	GlmTests-class
pool2,SingleSnpTestsScore,SingleSnpTestsScore,logical-method	SingleSnpTests-class
post2g	mean2g
pp	pp
qq.chisq	qq.chisq
random.snps	random.snps
rbind,SnpMatrix-method	SnpMatrix-class
rbind2,SnpMatrix,SnpMatrix-method	SnpMatrix-class
read.beagle	read.beagle
read.impute	read.impute
read.long	read.long
read.mach	read.mach
read.pedfile	read.pedfile
read.plink	read.plink
read.snps.long	read.snps.long
row.summary	row.summary
sample-long-alleles.gz	sample
sample-long.gz	sample
sample.bed	sample
sample.bim	sample
sample.fam	sample
sample.info	sample
sample.size	chi.squared
sample.size,GlmTests-method	GlmTests-class
sample.size,SingleSnpTests-method	SingleSnpTests-class
show,GlmEstimates-method	GlmEstimates-class
show,GlmTests-method	GlmTests-class
show,ImputationRules-method	ImputationRules-class
show,SingleSnpTests-method	SingleSnpTests-class
show,SnpMatrix-method	SnpMatrix-class
show,XSnpMatrix-method	XSnpMatrix-class
single.snp.tests	single.snp.tests
SingleSnpTests-class	SingleSnpTests-class
SingleSnpTestsScore-class	SingleSnpTests-class
sm.compare	sm.compare
snp.cor	snp.cor
snp.imputation	snp.imputation
snp.lhs.estimates	snp.lhs.estimates
snp.lhs.tests	snp.lhs.tests
snp.post.multiply	snp.pre.multiply
snp.pre.multiply	snp.pre.multiply
snp.rhs.estimates	snp.rhs.estimates
snp.rhs.tests	snp.rhs.tests
snp.support	for.exercise
SnpMatrix-class	SnpMatrix-class
snps.10	for.exercise
snpStats	snpStats-package
subject.data	testdata
subject.support	for.exercise
summary,GlmTests-method	GlmTests-class
summary,ImputationRules-method	ImputationRules-class
summary,SingleSnpTests-method	SingleSnpTests-class
summary,SnpMatrix-method	SnpMatrix-class
summary,XSnpMatrix-method	XSnpMatrix-class
support.ld	ld.example
switch.alleles	switch.alleles
switch.alleles,GlmTestsScore,character-method	GlmTests-class
switch.alleles,SingleSnpTestsScore,ANY-method	SingleSnpTests-class
switch.alleles,SnpMatrix,ANY-method	SnpMatrix-class
tdt.snp	tdt.snp
test.allele.switch	test.allele.switch
testdata	testdata
write.plink	write.plink
write.SnpMatrix	write.snp.matrix
Xchromosome	testdata
XSnpMatrix-class	XSnpMatrix-class
Xsnps	testdata
xxt	xxt
yri.1mb	ld.example
[,GlmEstimates,ANY,missing,missing-method	GlmEstimates-class
[,GlmTests,ANY,missing,missing-method	GlmTests-class
[,GlmTestsScore,ANY,missing,missing-method	GlmTests-class
[,ImputationRules,ANY,missing,missing-method	ImputationRules-class
[,SingleSnpTests,ANY,missing,missing-method	SingleSnpTests-class
[,SingleSnpTestsScore,ANY,missing,missing-method	SingleSnpTests-class
[,SnpMatrix,ANY,ANY,ANY-method	SnpMatrix-class
[,XSnpMatrix,ANY,ANY,ANY-method	XSnpMatrix-class
[<-,XSnpMatrix,ANY,ANY,XSnpMatrix-method	XSnpMatrix-class
