# SnpMatrix and XSnpMatrix classes and methods

## Documentation for package ‘snpStats’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

snpStats-package | 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 --

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"