snpMatrix-package {snpMatrix} | R Documentation

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

### Description

Implements classes and some basic methods for large-scale SNP association studies

### Details

Package: | snpMatrix
Version: | 1.4.1
Date: | 2008-06-05
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 indata.R ld.snp.R ld.with.R.eml.R misc.R outdata.R qq_chisq.R read.chiamo.R read.HapMap.R read.snps.pedfile.R single.R structure.R wtccc.sample.list.R wtccc.signals.R xstuff.R zzz.R
LazyLoad: | yes
biocViews: | Microarray, SNPsAndGeneticVariability
Packaged: | Thu, June 5, 2008; David Clayton
Built: | R 2.7.0; x86_64-pc-linux-gnu; 2008-06-06 11:36:17; unix

Index:

    X.snp-class             Class "X.snp"
    X.snp.matrix-class      Class "X.snp.matrix"
    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
    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)
    ld.snp                  Function to calculate pairwise D', $r^2$
    ld.with                 function to calculate the LD measures of
                            specific SNPs against other SNPs
    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
    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.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
    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.pre                 Pre- or post-multiply a snp.matrix object by a
                            general matrix
    snp.rhs.tests           Score tests with SNP genotypes as independent
                            variable
    snpMatrix-package       The snp.matrix and X.snp.matrix classes
    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 normalised snp.matrix

Further information is available in the following vignettes:

`snpMatrix-vignette` | snpMatrix (source)

### 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 1.4.2 Index]