snpMatrix (version 1.19.24)

snpMatrix-package: The snp.matrix and X.snp.matrix classes

Description

Implements classes and some basic methods for large-scale SNP association studies

Details

ll{ Package: snpMatrix Version: 1.2.4 Date: 2008-03-17 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 indata.R ld.snp.R ld.with.R.eml.R misc.R outdata.R qq_chisq.R read.chiamo.R read.HapMap.R read.snps.pedfile.R single.R structure.R wtccc.sample.list.R wtccc.signals.R xstuff.R zzz.R LazyLoad: yes biocViews: Microarray, SNPsAndGeneticVariability Packaged: Mon Mar 17 11:46:30 2008; david Built: R 2.7.0; i686-pc-linux-gnu; 2008-03-17 11:47:01; unix }

Index: X.snp-class Class "X.snp" X.snp.matrix-class Class "X.snp.matrix" epsout.ld.snp Function to write an eps file directly to visualize LD 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) ld.snp Function to calculate pairwise D', $r^2$ ld.with function to calculate the LD measures of specific SNPs against other SNPs pair.result.ld.snp Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs plot.snp.dprime Function to draw the pairwise D' in a eps file 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.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 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.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.rhs.tests Score tests with SNP genotypes as independent variable snpMatrix-package The snp.matrix and X.snp.matrix classes 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 normalised snp.matrix

Further information is available in the following vignettes: ll{ snpMatrix-vignette snpMatrix (source, pdf) }