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:    1.7.8
       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)

_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>

