Package: chopsticks 1.79.0

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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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
chopsticks/json (API)

# Install 'chopsticks' in R:

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

Datasets:

Asnps - Test data for the snpMatrix package
Autosomes - 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
Xchromosome - Test data for the snpMatrix package
Xsnps - Test data for the snpMatrix package

On BioConductor:chopsticks-1.79.0(bioc 3.24)chopsticks-1.78.0(bioc 3.23)

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

microarray snpsandgeneticvariability snp geneticvariability

3.48 score 6 scripts 1 mentions 38 exports 3 dependencies

Last updated from:e86f3e6c40. Checks:1 ERROR, 10 WARNING, 2 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	160
linux-devel-arm64	WARNING	155
linux-devel-x86_64	WARNING	149
source / vignettes	OK	310
linux-release-arm64	WARNING	158
linux-release-x86_64	WARNING	159
macos-release-arm64	WARNING	88
macos-release-x86_64	WARNING	201
macos-oldrel-arm64	FAIL	76
macos-oldrel-x86_64	WARNING	171
windows-devel	WARNING	109
windows-release	WARNING	113
windows-oldrel	WARNING	122
wasm-release	OK	107

Exports:cbind2 coerce convert.snpMatrix convert.snpMatrix.dir epsout.ld.snp glm.test.control ibs.stats ibsCount ibsDist initialize ld.snp ld.with niceprint pair.result.ld.snp plot.snp.dprime print.snp.dprime qq.chisq rbind2 read.HapMap.data read.pedfile.info read.snps.chiamo read.snps.long read.snps.long.old read.snps.pedfile read.wtccc.signals row.summary show single.snp.tests snp.cbind snp.cor snp.lhs.tests snp.post snp.pre snp.rbind snp.rhs.tests summary write.snp.matrix xxt

Dependencies:lattice Matrix survival

snpMatrix

Rendered fromchopsticks-vignette.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The snp.matrix and X.snp.matrix classes	snpMatrix-package snpMatrix
Function to write an eps file directly to visualize LD	epsout.ld.snp
Data for exercise in use of the snpMatrix package	for.exercise snp.support snps.10 subject.support
Set up control object for GLM tests	glm.test.control
function to calculate the identity-by-state stats of a group of samples	ibs.stats
Count alleles identical by state	ibsCount
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 SNPs	ld.with ld.with,snp.matrix,character-method
Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs	pair.result.ld.snp
Function to draw the pairwise D' in a eps file	plot.snp.dprime
Quantile-quantile plot for chi-squared tests	qq.chisq
function to import HapMap genotype data as snp.matrix	read.HapMap.data
function to read the accompanying info file of a LINKAGE ped file	read.pedfile.info
function to read the accompanying map file of a LINKAGE ped file	read.pedfile.map
Read genotype data from the output of Chiamo	read.snps.chiamo
Read SNP data in long format	read.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 format	read.wtccc.signals
Summarize rows of a snp matrix	row.summary
1-df and 2-df tests for genetic associations with SNPs	single.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 objects	cbind cbind2 rbind rbind2 snp.cbind snp.rbind
Correlations with columns of a snp.matrix	snp.cor
Class "snp.dprime" for Results of LD calculation	niceprint print.snp.dprime snp.dprime-class
Score tests with SNP genotypes as dependent variable	snp.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 matrix	snp.post snp.pre
Score tests with SNP genotypes as independent variable	snp.rhs.tests
snpMatrix-internal	convert.snpMatrix convert.snpMatrix.dir genotype-class haplotype-class
Test data for the snpMatrix package	Asnps Autosomes subject.data testdata Xchromosome Xsnps
Write a snp.matrix object as a text file	write.snp.matrix
read the sample list from the header of the WTCCC signal file format	wtccc.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.matrix	xxt