# The snp.matrix and X.snp.matrix classes

## Documentation for package ‘chopsticks’ version 1.16.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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

chopsticks-package | The snp.matrix and X.snp.matrix classes

## -- A --

Asnps | Test data for the chopsticks package
Autosomes | Test data for the chopsticks package

## -- C --

cbind | Bind together two or more snp.matrix objects
cbind-method | Class "snp.matrix"
cbind2 | Bind together two or more snp.matrix objects
cbind2-method | Class "snp.matrix"
chi.squared | Extract test statistics and p-values
chi.squared-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
chi.squared-method | Classes "snp.tests.single" and "snp.tests.single.score"
chopsticks | The snp.matrix and X.snp.matrix classes
coerce-method | Class "X.snp"
coerce-method | Class "X.snp.matrix"
coerce-method | Class "snp"
coerce-method | Class "snp.matrix"
coerce-method | Classes "snp.tests.single" and "snp.tests.single.score"
col.summary | Summarize rows or columns of a snp matrix

## -- D --

deg.freedom | Extract test statistics and p-values
deg.freedom-method | Classes "snp.tests.glm" and "snp.tests.glm.score"

## -- E --

effect.sign | Extract test statistics and p-values
effect.sign-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
effect.sign-method | Classes "snp.tests.single" and "snp.tests.single.score"
effective.sample.size | Extract test statistics and p-values
effective.sample.size-method | Classes "snp.tests.single" and "snp.tests.single.score"
epsout.ld.snp | Function to write an eps file directly to visualize LD
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 chopsticks package
Fst | Calculate fixation indices

## -- G --

genotype-class | chopsticks-internal
genotypes | Test data for family association tests
Genotypes.GenTrain1 | function to do compare two snp.matrix class object
Genotypes.GenTrain2 | function to do compare two snp.matrix class object
GenTrain1 | function to do compare two snp.matrix class object
GenTrain2 | function to do compare two snp.matrix class object
glm.test.control | Set up control object for GLM tests

## -- H --

haplotype-class | chopsticks-internal

## -- I --

ibs.stats | function to calculate the identity-by-state stats of a group of samples
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
impute.snps | Impute snps
initialize-method | Class "X.snp.matrix"
initialize-method | Class "snp.matrix"
is.na-method | Class "snp.matrix"

## -- L --

ld.snp | Function to calculate pairwise D', r-squared
ld.with | function to calculate the LD measures of specific SNPs against other SNPs
ld.with-method | function to calculate the LD measures of specific SNPs against other SNPs

## -- M --

misinherits | Find non-Mendelian inheritances in family data

## -- N --

names-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
names-method | Classes "snp.tests.single" and "snp.tests.single.score"
niceprint | Class "snp.dprime" for Results of LD calculation

## -- P --

p.value | Extract test statistics and p-values
p.value-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
p.value-method | Classes "snp.tests.single" and "snp.tests.single.score"
pair.result.ld.snp | Function to calculate the pairwise D', r-squared, LOD of a pair of specified SNPs
pedfile | Test data for family association tests
plot-method | Class "snp.reg.imputation"
plot.snp.dprime | Function to draw the pairwise D' in a eps file
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 "snp.tests.glm" and "snp.tests.glm.score"
pool2-method | Classes "snp.tests.single" and "snp.tests.single.score"
print.snp.dprime | Class "snp.dprime" for Results of LD calculation

## -- Q --

qq.chisq | Quantile-quantile plot for chi-squared tests

## -- R --

rbind | Bind together two or more snp.matrix objects
rbind-method | Class "snp.matrix"
rbind2 | Bind together two or more snp.matrix objects
rbind2-method | Class "snp.matrix"
read.beagle | Read genotypes imputed by the BEAGLE program
read.HapMap.data | function to import HapMap genotype data as snp.matrix
read.impute | Read genotypes imputed by the IMPUTE2 program
read.mach | Read genotypes imputed by the MACH program
read.pedfile.info | function to read the accompanying info file of a LINKAGE ped file
read.pedfile.map | function to read the accompanying map file of a LINKAGE ped file
read.plink | Read a PLINK binary data file as a snp.matrix
read.snps.chiamo | Read genotype data from the output of Chiamo
read.snps.long | Read SNP data in long format
read.snps.pedfile | Read genotype data from a LINKAGE "pedfile"
read.wtccc.signals | read normalized signals in the WTCCC signal file format
row.summary | Summarize rows or columns of a snp matrix

## -- S --

sample.size | Extract test statistics and p-values
sample.size-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
sample.size-method | Classes "snp.tests.single" and "snp.tests.single.score"
show-method | Class "X.snp"
show-method | Class "X.snp.matrix"
show-method | Class "snp"
show-method | Class "snp.estimates.glm"
show-method | Class "snp.matrix"
show-method | Class "snp.reg.imputation"
show-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
show-method | Classes "snp.tests.single" and "snp.tests.single.score"
single.snp.tests | 1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs)
snp-class | Class "snp"
snp.cbind | Bind together two or more snp.matrix objects
snp.clust.plot | function to do colorized cluster plots
snp.compare | function to do compare two snp.matrix class object
snp.cor | Correlations with columns of a snp.matrix
snp.dprime-class | Class "snp.dprime" for Results of LD calculation
snp.estimates.glm-class | Class "snp.estimates.glm"
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.matrix-class | Class "snp.matrix"
snp.post.multiply | Pre- or post-multiply a snp.matrix object by a general matrix
snp.pre.multiply | Pre- or post-multiply a snp.matrix object by a general matrix
snp.rbind | Bind together two or more snp.matrix objects
snp.reg.imputation-class | Class "snp.reg.imputation"
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 chopsticks package
snp.tests.glm-class | Classes "snp.tests.glm" and "snp.tests.glm.score"
snp.tests.glm.score-class | Classes "snp.tests.glm" and "snp.tests.glm.score"
snp.tests.single-class | Classes "snp.tests.single" and "snp.tests.single.score"
snp.tests.single.score-class | Classes "snp.tests.single" and "snp.tests.single.score"
snps.10 | Data for exercise in use of the chopsticks package
subject.data | Test data for the chopsticks package
subject.support | Data for exercise in use of the chopsticks package
summary-method | Class "X.snp.matrix"
summary-method | Class "snp.matrix"
summary-method | Class "snp.reg.imputation"
summary-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
summary-method | Classes "snp.tests.single" and "snp.tests.single.score"
switch.alleles | Switch alleles in columns of a snp.matrix or in test results
switch.alleles-method | Class "snp.matrix"
switch.alleles-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
switch.alleles-method | Classes "snp.tests.single" and "snp.tests.single.score"

## -- 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 chopsticks package

## -- W --

write.plink | Write files for analysis in the PLINK toolset
write.snp.matrix | Write a snp.matrix object as a text file
wtccc.sample.list | read the sample list from the header of the WTCCC signal file format

## -- X --

X.snp-class | Class "X.snp"
X.snp.matrix-class | Class "X.snp.matrix"
Xchromosome | Test data for the chopsticks package
Xsnps | Test data for the chopsticks package
xxt | X.X-transpose for a standardized snp.matrix

## -- misc --

[-method | Class "X.snp.matrix"
[-method | Class "snp.estimates.glm"
[-method | Class "snp.matrix"
[-method | Class "snp.reg.imputation"
[-method | Classes "snp.tests.glm" and "snp.tests.glm.score"
[-method | Classes "snp.tests.single" and "snp.tests.single.score"
[<--method | Class "X.snp.matrix"