\name{snpMatrix-package}
\alias{snpMatrix-package}
\alias{snpMatrix}
\docType{package}
\title{
The snp.matrix and X.snp.matrix classes
}
\description{
Implements classes and methods for large-scale SNP association studies
}
\details{
\tabular{ll}{
Package: \tab snpMatrix\cr
Version: \tab 1.7.8\cr
Date: \tab 2009-04-17\cr
Depends: \tab R(>= 2.3.0), survival, methods\cr
Suggests: \tab hexbin\cr
Enhances: \tab genetics\cr
License: \tab GNU General Public Licence (GPLv3)\cr
URL: \tab http://www-gene.cimr.cam.ac.uk/clayton/software/\cr
Collate: \tab ld.with.R ss.R contingency.table.R glm-test.R ibs.stats.R imputation.R indata.R ld.snp.R ld.with.R.eml.R misc.R outdata.R plink.R qc.R qq-chisq.R read.chiamo.R read.HapMap.R read.snps.pedfile.R single.R tdt-single.R structure.R wtccc.sample.list.R wtccc.signals.R xstuff.R zzz.R\cr
LazyLoad: \tab yes\cr
biocViews: \tab Microarray, SNPsAndGeneticVariability\cr
Built: \tab R 2.8.1; x86\_64-pc-linux-gnu; 2009-04-17 09:49:40; unix\cr
}

Index:
\preformatted{
X.snp-class             Class "X.snp"
X.snp.matrix-class      Class "X.snp.matrix"
chi.squared             Extract test statistics and p-values
epsout.ld.snp           Function to write an eps file directly to
                        visualize LD
families                Test data for family association tests
filter.rules            Filter a set of imputation rules
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
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 MAF and R-squared values from
                        imputation rules
impute.snps             Impute snps
ld.snp                  Function to calculate pairwise D', r-squared
ld.with                 function to calculate the LD measures of
                        specific SNPs against other SNPs
misinherits             Find non-Mendelian inheritances in family data
pair.result.ld.snp      Function to calculate the pairwise D',
                        r-squared, LOD of a pair of specified SNPs
plot.snp.dprime         Function to draw the pairwise D' in a eps file
pool                    Pool test results from several studies or
                        sub-studies
pool2                   Pool results of tests from two independent
                        datasets
qq.chisq                Quantile-quantile plot for chi-squared tests
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.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
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.cor                 Correlations with columns of a snp.matrix
snp.dprime-class        Class "snp.dprime" for Results of LD
                        calculation
snp.imputation          Calculate imputation rules
snp.lhs.tests           Score tests with SNP genotypes as dependent
                        variable
snp.matrix-class        Class "snp.matrix"
snp.pre                 Pre- or post-multiply a snp.matrix object by a
                        general matrix
snp.reg.imputation-class
                        Class "snp.reg.imputation"
snp.rhs.tests           Score tests with SNP genotypes as independent
                        variable
snp.tests.glm-class     Classes "snp.tests.glm" and
                        "snp.tests.glm.score"
snp.tests.single-class
                        Classes "snp.tests.single" and
                        "snp.tests.single.score"
snpMatrix-package       The snp.matrix and X.snp.matrix classes
switch.alleles          Switch alleles in columns of a snp.matrix or in
                        test results
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 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
xxt                     X.X-transpose for a standardized snp.matrix
}

Further information is available in the following vignettes:
\tabular{ll}{
\code{imputation-vignette} \tab Imputation and meta-analysis (source, pdf)\cr
\code{pca-vignette} \tab Principal components analysis (source, pdf)\cr
\code{snpMatrix-vignette} \tab snpMatrix introduction (source, pdf)\cr
\code{tdt-vignette} \tab TDT tests (source, pdf)\cr
}
}
\author{
David Clayton <david.clayton@cimr.cam.ac.uk> and
Hin-Tak Leung <htl10@users.sourceforge.net>

Maintainer: David Clayton <david.clayton@cimr.cam.ac.uk>
}
\keyword{ package }