Classes and statistical methods for large SNP association studies, extending the snpMatrix package
|Depends:||R(>= 2.10.0), survival, Matrix, methods|
|Imports:||graphics, grDevices, stats, utils, BiocGenerics, zlibbioc|
|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|
|biocViews:||Microarray, SNP, GeneticVariability|
|Built:||R 3.1.1; x86_64-pc-linux-gnu; 2014-08-17 12:28:22 UTC; unix|
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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 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
David Clayton <[email protected]>
Maintainer: David Clayton <[email protected]>
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