snpStats-package {snpStats} | R Documentation

## SnpMatrix and XSnpMatrix classes and methods

### Description

Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

### Details

The DESCRIPTION file:

Package: | snpStats
Title: | SnpMatrix and XSnpMatrix classes and methods
Version: | 1.40.0
Date: | 2019-10-08
Author: | David Clayton <dc208@cam.ac.uk>
Description: | Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.
Maintainer: | David Clayton <dc208@cam.ac.uk>
Depends: | R(>= 2.10.0), survival, Matrix, methods
Imports: | graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
Suggests: | hexbin
License: | GPL-3
Collate: | ss.R contingency.table.R convert.R compare.R glm-test.R imputation.R indata.R long.R misc.R ld.R mvtests.R pedfile.R outdata.R plink.R qc.R qq-chisq.R single.R tdt-single.R structure.R xstuff.R
LazyLoad: | yes
biocViews: | Microarray, SNP, GeneticVariability
Packaged: | 2019-10-08
git_url: | https://git.bioconductor.org/packages/snpStats
git_branch: | RELEASE_3_12
git_last_commit: | 5fcac6f
git_last_commit_date: | 2020-10-27
Date/Publication: | 2020-10-28

Index of help topics:

    Fst                     Calculate fixation indices
    GlmEstimates-class      Class "GlmEstimates"
    GlmTests-class          Classes "GlmTests" and "GlmTestsScore"
    ImputationRules-class   Class "ImputationRules"
    SingleSnpTests-class    Classes "SingleSnpTests" and
                            "SingleSnpTestsScore"
    SnpMatrix-class         Class "SnpMatrix"
    XSnpMatrix-class        Class "XSnpMatrix"
    chi.squared             Extract test statistics and p-values
    convert.snpMatrix       Convert 'snpMatrix' objects to 'snpStats'
                            objects
    example-new             An example of intensity data for SNP genotyping
    families                Test data for family association tests
    filter.rules            Filter a set of imputation rules
    for.exercise            Data for exercise in use of the snpStats
                            package
    glm.test.control        Set up control object for GLM computations
    ibsCount                Count alleles identical by state
    ibsDist                 Distance matrix based on identity by state
                            (IBS)
    imputation.maf          Extract statistics from imputation rules
    impute.snps             Impute snps
    ld                      Pairwise linkage disequilibrium measures
    ld.example              Datasets to illustrate calculation of linkage
                            disequilibrium statistics
    mean2g                  Raw coding of posterior probabilities of SNP
                            genotype
    misinherits             Find non-Mendelian inheritances in family data
    mvtests                 Multivariate SNP tests
    plotUncertainty         Plot posterior probabilities of genotype
                            assignment
    pool                    Pool test results from several studies or
                            sub-studies
    pool2                   Pool results of tests from two independent
                            datasets
    pp                      Unpack posterior probabilities from one-byte
                            codes
    qq.chisq                Quantile-quantile plot for chi-squared tests
    random.snps             Generate random SnpMatrix
    read.beagle             Read genotypes imputed by the BEAGLE program
    read.impute             Read genotypes imputed by the IMPUTE2 program
    read.long               Read SNP genotype data in long format
    read.mach               Read genotypes imputed by the MACH program
    read.pedfile            Read a pedfile as '"SnpMatrix"' object
    read.plink              Read a PLINK binary data file as a SnpMatrix
    read.snps.long          Read SNP data in long format (deprecated)
    row.summary             Summarize rows or columns of a snp matrix
    sample.info             Sample datasets to illustrate data input
    single.snp.tests        1-df and 2-df tests for genetic associations
                            with SNPs (or imputed SNPs)
    sm.compare              Compare two SnpMatrix objects
    snp.cor                 Correlations with columns of a SnpMatrix
    snp.imputation          Calculate imputation rules
    snp.lhs.estimates       Logistic regression with SNP genotypes as
                            dependent variable
    snp.lhs.tests           Score tests with SNP genotypes as dependent
                            variable
    snp.pre.multiply        Pre- or post-multiply a SnpMatrix object by a
                            general matrix
    snp.rhs.estimates       Fit GLMs with SNP genotypes as independent
                            variable(s)
    snp.rhs.tests           Score tests with SNP genotypes as independent
                            variable
    snpStats-package        SnpMatrix and XSnpMatrix classes and methods
    switch.alleles          Switch alleles in columns of a SnpMatrix 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 snpStats package
    write.SnpMatrix         Write a SnpMatrix object as a text file
    write.plink             Write files for analysis in the PLINK toolset
    xxt                     X.X-transpose for a standardized SnpMatrix

### Author(s)

David Clayton <dc208@cam.ac.uk>

Maintainer: David Clayton <dc208@cam.ac.uk>

[Package snpStats version 1.40.0 Index]