snpMatrix-package         package:snpMatrix         R Documentation

_T_h_e _s_n_p._m_a_t_r_i_x _a_n_d _X._s_n_p._m_a_t_r_i_x _c_l_a_s_s_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Implements classes and methods for large-scale SNP association
     studies

_D_e_t_a_i_l_s:


       Package:    snpMatrix
       Version:    1.5.6
       Date:       2008-10-09
       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
       Packaged:   Wed Oct 15 10:55:50 BST 2008
       Built:      R 2.7.1; x86_64-redhat-linux-gnu; 2008-10-15 10:53:33; 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.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 (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 regression-based 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 (source, pdf)
       'snpMatrix-vignette'   snpMatrix (source, pdf)

_A_u_t_h_o_r(_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>

