snpMatrix-package {snpMatrix} | R Documentation

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

### Description

Implements classes and methods for large-scale SNP association studies

### Details

Package: | snpMatrix
Version: | 1.7.8
Date: | 2009-04-17
Depends: | R(>= 2.3.0), survival, methods
Suggests: | hexbin
Enhances: | genetics
License: | GNU General Public Licence (GPLv3)
URL: | http://www-gene.cimr.cam.ac.uk/clayton/software/
Collate: | 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
LazyLoad: | yes
biocViews: | Microarray, SNPsAndGeneticVariability
Built: | R 2.8.1; x86_64-pc-linux-gnu; 2009-04-17 09:49:40; unix

Index:

    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:

`imputation-vignette` | Imputation and meta-analysis (source, pdf)
`pca-vignette` | Principal components analysis (source, pdf)
`snpMatrix-vignette` | snpMatrix introduction (source, pdf)
`tdt-vignette` | TDT tests (source, pdf)

### Author(s)

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>

[Package snpMatrix version 1.8.0 Index]