Package: chopsticks 1.71.0

Hin-Tak Leung

chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

Implements classes and methods for large-scale SNP association studies

Authors:Hin-Tak Leung <[email protected]>

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# Install 'chopsticks' in R:
install.packages('chopsticks', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Asnps - Test data for the snpMatrix package
  • Autosomes - Test data for the snpMatrix package
  • Xchromosome - Test data for the snpMatrix package
  • Xsnps - Test data for the snpMatrix package
  • snp.support - Data for exercise in use of the snpMatrix package
  • snps.10 - Data for exercise in use of the snpMatrix package
  • subject.data - Test data for the snpMatrix package
  • subject.support - Data for exercise in use of the snpMatrix package

On BioConductor:chopsticks-1.71.0(bioc 3.20)chopsticks-1.70.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

38 exports 1.08 score 3 dependencies 1 mentions

Last updated 2 months agofrom:37ef827e8e

Exports:cbind2coerceconvert.snpMatrixconvert.snpMatrix.direpsout.ld.snpglm.test.controlibs.statsibsCountibsDistinitializeld.snpld.withniceprintpair.result.ld.snpplot.snp.dprimeprint.snp.dprimeqq.chisqrbind2read.HapMap.dataread.pedfile.inforead.snps.chiamoread.snps.longread.snps.long.oldread.snps.pedfileread.wtccc.signalsrow.summaryshowsingle.snp.testssnp.cbindsnp.corsnp.lhs.testssnp.postsnp.presnp.rbindsnp.rhs.testssummarywrite.snp.matrixxxt

Dependencies:latticeMatrixsurvival

snpMatrix

Rendered fromchopsticks-vignette.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
The snp.matrix and X.snp.matrix classessnpMatrix-package snpMatrix
Function to write an eps file directly to visualize LDepsout.ld.snp
Data for exercise in use of the snpMatrix packagefor.exercise snp.support snps.10 subject.support
Set up control object for GLM testsglm.test.control
function to calculate the identity-by-state stats of a group of samplesibs.stats
Count alleles identical by stateibsCount
Distance matrix based on identity by state (IBS)ibsDist
Function to calculate pairwise D', $r^2$ld.snp
function to calculate the LD measures of specific SNPs against other SNPsld.with ld.with,snp.matrix,character-method
Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPspair.result.ld.snp
Function to draw the pairwise D' in a eps fileplot.snp.dprime
Quantile-quantile plot for chi-squared testsqq.chisq
function to import HapMap genotype data as snp.matrixread.HapMap.data
function to read the accompanying info file of a LINKAGE ped fileread.pedfile.info
function to read the accompanying map file of a LINKAGE ped fileread.pedfile.map
Read genotype data from the output of Chiamoread.snps.chiamo
Read SNP data in long formatread.snps.long
Read SNP input data in "long" format (old version)read.snps.long.old
Read genotype data from a LINKAGE "pedfile"read.snps.pedfile
read normalized signals in the WTCCC signal file formatread.wtccc.signals
Summarize rows of a snp matrixrow.summary
1-df and 2-df tests for genetic associations with SNPssingle.snp.tests
Class "snp"coerce,snp,character-method coerce,snp,genotype-method coerce,snp,numeric-method show,snp-method snp-class
Bind together two or more snp.matrix objectscbind cbind2 rbind rbind2 snp.cbind snp.rbind
Correlations with columns of a snp.matrixsnp.cor
Class "snp.dprime" for Results of LD calculationniceprint print.snp.dprime snp.dprime-class
Score tests with SNP genotypes as dependent variablesnp.lhs.tests
Class "snp.matrix"cbind,snp.matrix-method cbind2,snp.matrix,snp.matrix-method coerce,matrix,snp.matrix-method coerce,snp.matrix,character-method coerce,snp.matrix,numeric-method initialize,snp.matrix-method is.na,snp.matrix-method rbind,snp.matrix-method rbind2,snp.matrix,snp.matrix-method show,snp.matrix-method snp.matrix-class summary,snp.matrix-method [,snp.matrix,ANY,ANY,ANY-method [,snp.matrix-method [,X.snp.matrix,ANY,ANY,ANY-method
Pre- or post-multiply a snp.matrix object by a general matrixsnp.post snp.pre
Score tests with SNP genotypes as independent variablesnp.rhs.tests
snpMatrix-internalconvert.snpMatrix convert.snpMatrix.dir genotype-class haplotype-class
Test data for the snpMatrix packageAsnps Autosomes subject.data testdata Xchromosome Xsnps
Write a snp.matrix object as a text filewrite.snp.matrix
read the sample list from the header of the WTCCC signal file formatwtccc.sample.list
Class "X.snp"coerce,X.snp,character-method coerce,X.snp,genotype-method coerce,X.snp,numeric-method show,X.snp-method X.snp-class
Class "X.snp.matrix"coerce,snp.matrix,X.snp.matrix-method coerce,X.snp.matrix,character-method initialize,X.snp.matrix-method show,X.snp.matrix-method summary,X.snp.matrix-method X.snp.matrix-class [,X.snp.matrix-method [<-,X.snp.matrix,ANY,ANY,X.snp.matrix-method
X.X-transpose for a normalised snp.matrixxxt