snpMatrix-package	snpMatrix-package
Asnps	testdata
Autosomes	testdata
cbind	snp.cbind
cbind,snp.matrix-method	snp.matrix-class
cbind2	snp.cbind
cbind2,snp.matrix,snp.matrix-method	snp.matrix-class
chi.squared	chi.squared
chi.squared,snp.tests.glm,missing-method	snp.tests.glm-class
chi.squared,snp.tests.single,numeric-method	snp.tests.single-class
coerce,matrix,snp.matrix-method	snp.matrix-class
coerce,snp,character-method	snp-class
coerce,snp,genotype-method	snp-class
coerce,snp,numeric-method	snp-class
coerce,snp.matrix,character-method	snp.matrix-class
coerce,snp.matrix,numeric-method	snp.matrix-class
coerce,snp.matrix,X.snp.matrix-method	X.snp.matrix-class
coerce,snp.tests.single,data.frame-method	snp.tests.single-class
coerce,X.snp,character-method	X.snp-class
coerce,X.snp,genotype-method	X.snp-class
coerce,X.snp,numeric-method	X.snp-class
coerce,X.snp.matrix,character-method	X.snp.matrix-class
col.summary	row.summary
deg.freedom	chi.squared
deg.freedom,snp.tests.glm-method	snp.tests.glm-class
effect.sign	chi.squared
effect.sign,snp.tests.glm,logical-method	snp.tests.glm-class
effect.sign,snp.tests.single.score,missing-method	snp.tests.single-class
effective.sample.size	chi.squared
effective.sample.size,snp.tests.single-method	snp.tests.single-class
epsout.ld.snp	epsout.ld.snp
example-new	example-new
families	families
filter.rules	filter.rules
for.exercise	for.exercise
Fst	Fst
genotype-class	snpMatrix-internal
genotypes	families
glm.test.control	glm.test.control
haplotype-class	snpMatrix-internal
ibs.stats	ibs.stats
ibsCount	ibsCount
ibsDist	ibsDist
imputation.maf	imputation.maf
imputation.nsnp	imputation.maf
imputation.r2	imputation.maf
impute.snps	impute.snps
initialize,snp.matrix-method	snp.matrix-class
initialize,X.snp.matrix-method	X.snp.matrix-class
is.na,snp.matrix-method	snp.matrix-class
ld.snp	ld.snp
ld.with	ld.with
ld.with,snp.matrix,character-method	ld.with
misinherits	misinherits
names,snp.tests.glm-method	snp.tests.glm-class
names,snp.tests.single-method	snp.tests.single-class
niceprint	snp.dprime-class
p.value	chi.squared
p.value,snp.tests.glm,missing-method	snp.tests.glm-class
p.value,snp.tests.single,numeric-method	snp.tests.single-class
pair.result.ld.snp	pair.result.ld.snp
pedfile	families
plot,snp.reg.imputation,missing-method	snp.reg.imputation-class
plot.snp.dprime	plot.snp.dprime
pool	pool
pool2	pool2
pool2,snp.tests.glm.score,snp.tests.glm.score,logical-method	snp.tests.glm-class
pool2,snp.tests.single.score,snp.tests.single.score,logical-method	snp.tests.single-class
print.snp.dprime	snp.dprime-class
qq.chisq	qq.chisq
rbind	snp.cbind
rbind,snp.matrix-method	snp.matrix-class
rbind2	snp.cbind
rbind2,snp.matrix,snp.matrix-method	snp.matrix-class
read.HapMap.data	read.HapMap.data
read.pedfile.info	read.pedfile.info
read.pedfile.map	read.pedfile.map
read.plink	read.plink
read.snps.chiamo	read.snps.chiamo
read.snps.long	read.snps.long
read.snps.pedfile	read.snps.pedfile
read.wtccc.signals	read.wtccc.signals
row.summary	row.summary
sample.size	chi.squared
sample.size,snp.tests.glm-method	snp.tests.glm-class
sample.size,snp.tests.single-method	snp.tests.single-class
show,snp-method	snp-class
show,snp.estimates.glm-method	snp.estimates.glm-class
show,snp.matrix-method	snp.matrix-class
show,snp.reg.imputation-method	snp.reg.imputation-class
show,snp.tests.glm-method	snp.tests.glm-class
show,snp.tests.single-method	snp.tests.single-class
show,X.snp-method	X.snp-class
show,X.snp.matrix-method	X.snp.matrix-class
single.snp.tests	single.snp.tests
snp-class	snp-class
snp.cbind	snp.cbind
snp.clust.plot	snp.clust.plot
snp.compare	snp.compare
snp.cor	snp.cor
snp.dprime-class	snp.dprime-class
snp.estimates.glm-class	snp.estimates.glm-class
snp.imputation	snp.imputation
snp.lhs.estimates	snp.lhs.estimates
snp.lhs.tests	snp.lhs.tests
snp.matrix-class	snp.matrix-class
snp.post.multiply	snp.pre.multiply
snp.pre.multiply	snp.pre.multiply
snp.rbind	snp.cbind
snp.reg.imputation-class	snp.reg.imputation-class
snp.rhs.estimates	snp.rhs.estimates
snp.rhs.tests	snp.rhs.tests
snp.support	for.exercise
snp.tests.glm-class	snp.tests.glm-class
snp.tests.glm.score-class	snp.tests.glm-class
snp.tests.single-class	snp.tests.single-class
snp.tests.single.score-class	snp.tests.single-class
snpMatrix	snpMatrix-package
snps.10	for.exercise
subject.data	testdata
subject.support	for.exercise
summary,snp.matrix-method	snp.matrix-class
summary,snp.reg.imputation-method	snp.reg.imputation-class
summary,snp.tests.glm-method	snp.tests.glm-class
summary,snp.tests.single-method	snp.tests.single-class
summary,X.snp.matrix-method	X.snp.matrix-class
switch.alleles	switch.alleles
switch.alleles,snp.matrix,ANY-method	snp.matrix-class
switch.alleles,snp.tests.glm.score,character-method	snp.tests.glm-class
switch.alleles,snp.tests.single.score,ANY-method	snp.tests.single-class
tdt.snp	tdt.snp
test.allele.switch	test.allele.switch
testdata	testdata
write.snp.matrix	write.snp.matrix
wtccc.sample.list	wtccc.sample.list
X.snp-class	X.snp-class
X.snp.matrix-class	X.snp.matrix-class
Xchromosome	testdata
Xsnps	testdata
xxt	xxt
[,snp.estimates.glm,ANY,missing,missing-method	snp.estimates.glm-class
[,snp.matrix,ANY,ANY,ANY-method	snp.matrix-class
[,snp.matrix-method	snp.matrix-class
[,snp.reg.imputation,ANY,missing,missing-method	snp.reg.imputation-class
[,snp.tests.glm,ANY,missing,missing-method	snp.tests.glm-class
[,snp.tests.glm.score,ANY,missing,missing-method	snp.tests.glm-class
[,snp.tests.single,ANY,missing,missing-method	snp.tests.single-class
[,snp.tests.single.score,ANY,missing,missing-method	snp.tests.single-class
[,X.snp.matrix,ANY,ANY,ANY-method	X.snp.matrix-class
[,X.snp.matrix-method	X.snp.matrix-class
[<-,X.snp.matrix,ANY,ANY,X.snp.matrix-method	X.snp.matrix-class
