\name{chopsticks-package} \alias{chopsticks-package} \alias{chopsticks} \docType{package} \title{ The snp.matrix and X.snp.matrix classes } \description{ Implements classes and methods for large-scale SNP association studies } \details{ \tabular{ll}{ Package: \tab chopsticks\cr Version: \tab 1.15.5\cr Date: \tab 2011-01-24\cr Depends: \tab R(>= 2.3.0), survival, methods\cr Imports: \tab graphics, grDevices, methods, stats, survival, utils\cr Suggests: \tab hexbin\cr Enhances: \tab genetics\cr License: \tab GPL-3\cr URL: \tab http://sourceforge.net/projects/outmodedbonsai//software/\cr Collate: \tab 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 snp.compare.R tdt-single.R structure.R wtccc.sample.list.R wtccc.signals.R xstuff.R zzz.R\cr LazyLoad: \tab yes\cr biocViews: \tab Microarray, SNP, GeneticVariability\cr Built: \tab R 2.12.1; x86_64-pc-linux-gnu; 2011-01-24 14:46:45 UTC; unix\cr } Index: \preformatted{ Fst Calculate fixation indices 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 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 chopsticks package genotype-class chopsticks-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 statistics 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 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 qq.chisq Quantile-quantile plot for chi-squared tests read.HapMap.data function to import HapMap genotype data as snp.matrix read.beagle Read genotypes imputed by the BEAGLE program read.impute Read genotypes imputed by the IMPUTE2 program read.mach Read genotypes imputed by the MACH program 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.clust.plot function to do colorized cluster plots snp.compare function to do compare two snp.matrix class object snp.cor Correlations with columns of a snp.matrix snp.dprime-class Class "snp.dprime" for Results of LD calculation snp.estimates.glm-class Class "snp.estimates.glm" 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.matrix-class Class "snp.matrix" snp.pre.multiply Pre- or post-multiply a snp.matrix object by a general matrix snp.reg.imputation-class Class "snp.reg.imputation" snp.rhs.estimates Fit GLMs with SNP genotypes as independent variable(s) 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" chopsticks-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 chopsticks 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: \tabular{ll}{ \code{clustering-comparison-vignette} \tab Rill (source, pdf)\cr \code{imputation-vignette} \tab Imputation and meta-analysis (source, pdf)\cr \code{pca-vignette} \tab Principal components analysis (source, pdf)\cr \code{chopsticks-vignette} \tab chopsticks introduction (source, pdf)\cr \code{tdt-vignette} \tab TDT tests (source, pdf)\cr } } \author{ David Clayton \email{david.clayton@cimr.cam.ac.uk} and Hin-Tak Leung \email{htl10@users.sourceforge.net} Maintainer: David Clayton \email{david.clayton@cimr.cam.ac.uk} } \keyword{ package }