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

## Documentation for package ‘chopsticks’ version 1.40.0

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

## Help Pages

snpMatrix-package | The snp.matrix and X.snp.matrix classes
Asnps | Test data for the snpMatrix package
Autosomes | Test data for the snpMatrix package
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"
coerce-method | Class "X.snp"
coerce-method | Class "X.snp.matrix"
coerce-method | Class "snp"
coerce-method | Class "snp.matrix"
convert.snpMatrix | snpMatrix-internal
convert.snpMatrix.dir | snpMatrix-internal
epsout.ld.snp | Function to write an eps file directly to visualize LD
for.exercise | Data for exercise in use of the snpMatrix package
genotype-class | snpMatrix-internal
glm.test.control | Set up control object for GLM tests
haplotype-class | snpMatrix-internal
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)
initialize-method | Class "X.snp.matrix"
initialize-method | Class "snp.matrix"
is.na-method | Class "snp.matrix"
ld.snp | Function to calculate pairwise D', $r^2$
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
niceprint | Class "snp.dprime" for Results of LD calculation
pair.result.ld.snp | Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs
plot.snp.dprime | Function to draw the pairwise D' in a eps file
print.snp.dprime | Class "snp.dprime" for Results of LD calculation
qq.chisq | Quantile-quantile plot for chi-squared tests
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.HapMap.data | function to import HapMap genotype data as snp.matrix
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.snps.chiamo | Read genotype data from the output of Chiamo
read.snps.long | Read SNP data in long format
read.snps.long.old | Read SNP input data in "long" format (old version)
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 of a snp matrix
show-method | Class "X.snp"
show-method | Class "X.snp.matrix"
show-method | Class "snp"
show-method | Class "snp.matrix"
single.snp.tests | 1-df and 2-df tests for genetic associations with SNPs
snp-class | Class "snp"
snp.cbind | Bind together two or more snp.matrix objects
snp.cor | Correlations with columns of a snp.matrix
snp.dprime-class | Class "snp.dprime" for Results of LD calculation
snp.lhs.tests | Score tests with SNP genotypes as dependent variable
snp.matrix-class | Class "snp.matrix"
snp.post | Pre- or post-multiply a snp.matrix object by a general matrix
snp.pre | Pre- or post-multiply a snp.matrix object by a general matrix
snp.rbind | Bind together two or more snp.matrix objects
snp.rhs.tests | Score tests with SNP genotypes as independent variable
snp.support | Data for exercise in use of the snpMatrix package
snpMatrix | The snp.matrix and X.snp.matrix classes
snps.10 | Data for exercise in use of the snpMatrix package
subject.data | Test data for the snpMatrix package
subject.support | Data for exercise in use of the snpMatrix package
summary-method | Class "X.snp.matrix"
summary-method | Class "snp.matrix"
testdata | Test data for the snpMatrix package
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.snp-class | Class "X.snp"
X.snp.matrix-class | Class "X.snp.matrix"
Xchromosome | Test data for the snpMatrix package
Xsnps | Test data for the snpMatrix package
xxt | X.X-transpose for a normalised snp.matrix
[-method | Class "X.snp.matrix"
[-method | Class "snp.matrix"
[<--method | Class "X.snp.matrix"