SnpMatrix and XSnpMatrix classes and methods

Documentation for package ‘snpStats’ version 1.59.2

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A C D E F G I L M N P Q R S T W X Y misc

SnpMatrix and XSnpMatrix classes and methods

-- A --

Asnps	Test data for the snpStats package
Autosomes	Test data for the snpStats package

-- C --

can.impute	Extract statistics from imputation rules
cbind-method	Class "SnpMatrix"
cbind2-method	Class "SnpMatrix"
ceph.1mb	Datasets to illustrate calculation of linkage disequilibrium statistics
chi.squared	Extract test statistics and p-values
chi.squared-method	Classes "GlmTests" and "GlmTestsScore"
chi.squared-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
coerce-method	Class "GlmEstimates"
coerce-method	Classes "GlmTests" and "GlmTestsScore"
coerce-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
coerce-method	Class "SnpMatrix"
coerce-method	Class "XSnpMatrix"
col.summary	Summarize rows or columns of a snp matrix
convert.snpMatrix	Convert 'snpMatrix' objects to 'snpStats' objects
convert.snpMatrix.dir	Convert 'snpMatrix' objects to 'snpStats' objects

-- D --

deg.freedom	Extract test statistics and p-values
deg.freedom-method	Classes "GlmTests" and "GlmTestsScore"

-- E --

effect.sign	Extract test statistics and p-values
effect.sign-method	Classes "GlmTests" and "GlmTestsScore"
effect.sign-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
effective.sample.size	Extract test statistics and p-values
effective.sample.size-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
example-new	An example of intensity data for SNP genotyping

-- F --

families	Test data for family association tests
filter.rules	Filter a set of imputation rules
for.exercise	Data for exercise in use of the snpStats package
Fst	Calculate fixation indices

-- G --

g2post	Raw coding of posterior probabilities of SNP genotype
genotypes	Test data for family association tests
glm.test.control	Set up control object for GLM computations
GlmEstimates-class	Class "GlmEstimates"
GlmTests-class	Classes "GlmTests" and "GlmTestsScore"
GlmTestsScore-class	Classes "GlmTests" and "GlmTestsScore"

-- I --

ibsCount	Count alleles identical by state
ibsDist	Distance matrix based on identity by state (IBS)
imputation.maf	Extract statistics from imputation rules
imputation.nsnp	Extract statistics from imputation rules
imputation.r2	Extract statistics from imputation rules
ImputationRules-class	Class "ImputationRules"
impute.snps	Impute snps
initialize-method	Class "SnpMatrix"
initialize-method	Class "XSnpMatrix"
is.na-method	Class "SnpMatrix"

-- L --

ld	Pairwise linkage disequilibrium measures
ld.example	Datasets to illustrate calculation of linkage disequilibrium statistics

-- M --

mach1.out.mlprob.gz	Sample datasets to illustrate data input
mean2g	Raw coding of posterior probabilities of SNP genotype
misinherits	Find non-Mendelian inheritances in family data
mvtests	Multivariate SNP tests

-- N --

names-method	Classes "GlmTests" and "GlmTestsScore"
names-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"

-- P --

p.value	Extract test statistics and p-values
p.value-method	Classes "GlmTests" and "GlmTestsScore"
p.value-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
pedData	Test data for family association tests
plot-method	Class "ImputationRules"
plotUncertainty	Plot posterior probabilities of genotype assignment
pool	Pool test results from several studies or sub-studies
pool2	Pool results of tests from two independent datasets
pool2-method	Classes "GlmTests" and "GlmTestsScore"
pool2-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
post2g	Raw coding of posterior probabilities of SNP genotype
pp	Unpack posterior probabilities from one-byte codes

-- Q --

qq.chisq

Quantile-quantile plot for chi-squared tests

-- R --

random.snps	Generate random SnpMatrix
rbind-method	Class "SnpMatrix"
rbind2-method	Class "SnpMatrix"
read.beagle	Read genotypes imputed by the BEAGLE program
read.impute	Read genotypes imputed by the IMPUTE2 program
read.long	Read SNP genotype data in long format
read.mach	Read genotypes imputed by the MACH program
read.pedfile	Read a pedfile as '"SnpMatrix"' object
read.plink	Read a PLINK binary data file as a SnpMatrix
read.snps.long	Read SNP data in long format (deprecated)
row.summary	Summarize rows or columns of a snp matrix

-- S --

sample-long-alleles.gz	Sample datasets to illustrate data input
sample-long.gz	Sample datasets to illustrate data input
sample.bed	Sample datasets to illustrate data input
sample.bim	Sample datasets to illustrate data input
sample.fam	Sample datasets to illustrate data input
sample.info	Sample datasets to illustrate data input
sample.size	Extract test statistics and p-values
sample.size-method	Classes "GlmTests" and "GlmTestsScore"
sample.size-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
show-method	Class "GlmEstimates"
show-method	Classes "GlmTests" and "GlmTestsScore"
show-method	Class "ImputationRules"
show-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
show-method	Class "SnpMatrix"
show-method	Class "XSnpMatrix"
single.snp.tests	1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs)
SingleSnpTests-class	Classes "SingleSnpTests" and "SingleSnpTestsScore"
SingleSnpTestsScore-class	Classes "SingleSnpTests" and "SingleSnpTestsScore"
sm.compare	Compare two SnpMatrix objects
snp.cor	Correlations with columns of a SnpMatrix
snp.imputation	Calculate imputation rules
snp.lhs.estimates	Logistic regression with SNP genotypes as dependent variable
snp.lhs.tests	Score tests with SNP genotypes as dependent variable
snp.post.multiply	Pre- or post-multiply a SnpMatrix object by a general matrix
snp.pre.multiply	Pre- or post-multiply a SnpMatrix object by a general matrix
snp.rhs.estimates	Fit GLMs with SNP genotypes as independent variable(s)
snp.rhs.tests	Score tests with SNP genotypes as independent variable
snp.support	Data for exercise in use of the snpStats package
SnpMatrix-class	Class "SnpMatrix"
snps.10	Data for exercise in use of the snpStats package
snpStats	SnpMatrix and XSnpMatrix classes and methods
subject.data	Test data for the snpStats package
subject.support	Data for exercise in use of the snpStats package
summary-method	Classes "GlmTests" and "GlmTestsScore"
summary-method	Class "ImputationRules"
summary-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
summary-method	Class "SnpMatrix"
summary-method	Class "XSnpMatrix"
support.ld	Datasets to illustrate calculation of linkage disequilibrium statistics
switch.alleles	Switch alleles in columns of a SnpMatrix or in test results
switch.alleles-method	Classes "GlmTests" and "GlmTestsScore"
switch.alleles-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
switch.alleles-method	Class "SnpMatrix"

-- T --

tdt.snp	1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs) in family data
test.allele.switch	Test for switch of alleles between two collections
testdata	Test data for the snpStats package

-- W --

write.plink	Write files for analysis in the PLINK toolset
write.SnpMatrix	Write a SnpMatrix object as a text file

-- X --

Xchromosome	Test data for the snpStats package
XSnpMatrix-class	Class "XSnpMatrix"
Xsnps	Test data for the snpStats package
xxt	X.X-transpose for a standardized SnpMatrix

-- Y --

yri.1mb

Datasets to illustrate calculation of linkage disequilibrium statistics

-- misc --

[-method	Class "GlmEstimates"
[-method	Classes "GlmTests" and "GlmTestsScore"
[-method	Class "ImputationRules"
[-method	Classes "SingleSnpTests" and "SingleSnpTestsScore"
[-method	Class "SnpMatrix"
[-method	Class "XSnpMatrix"
[<--method	Class "XSnpMatrix"