chopsticks: The snp.matrix and X.snp.matrix classes
Version 1.40.0

Implements classes and methods for large-scale SNP association studies

Browse man pages Browse package API and functions Browse package files

AuthorHin-Tak Leung <htl10@users.sourceforge.net>
Bioconductor views GeneticVariability Microarray SNP SNPsAndGeneticVariability
Date of publicationNone
MaintainerHin-Tak Leung <htl10@users.sourceforge.net>
LicenseGPL-3
Version1.40.0
URL http://outmodedbonsai.sourceforge.net/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("chopsticks")

Man pages

epsout.ld.snp: Function to write an eps file directly to visualize LD
for.exercise: Data for exercise in use of the snpMatrix package
glm.test.control: Set up control object for GLM tests
ibsCount: Count alleles identical by state
ibsDist: Distance matrix based on identity by state (IBS)
ibs.stats: function to calculate the identity-by-state stats of a group...
ld.snp: Function to calculate pairwise D', $r^2$
ld.with: function to calculate the LD measures of specific SNPs...
pair.result.ld.snp: Function to calculate the pairwise D', $r^2$, LOD of a pair...
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...
read.pedfile.map: function to read the accompanying map file of a LINKAGE ped...
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.cbind: Bind together two or more snp.matrix objects
snp-class: Class "snp"
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"
snpMatrix-internal: snpMatrix-internal
snpMatrix-package: The snp.matrix and X.snp.matrix classes
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
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...
X.snp-class: Class "X.snp"
X.snp.matrix-class: Class "X.snp.matrix"
xxt: X.X-transpose for a normalised snp.matrix

Functions

Asnps Man page
Autosomes Man page
X.snp-class Man page
X.snp.matrix-class Man page
Xchromosome Man page
Xsnps Man page
[,X.snp.matrix-method Man page
[,snp.matrix-method Man page
[<-,X.snp.matrix,ANY,ANY,X.snp.matrix-method Man page
ast.lib Source code
cbind Man page
cbind,snp.matrix-method Man page
cbind2 Man page Source code
cbind2,snp.matrix,snp.matrix-method Man page
coerce,X.snp,character-method Man page
coerce,X.snp,genotype-method Man page
coerce,X.snp,numeric-method Man page
coerce,X.snp.matrix,character-method Man page
coerce,matrix,snp.matrix-method Man page
coerce,snp,character-method Man page
coerce,snp,genotype-method Man page
coerce,snp,numeric-method Man page
coerce,snp.matrix,X.snp.matrix-method Man page Man page
coerce,snp.matrix,character-method Man page
coerce,snp.matrix,numeric-method Man page
contingency.table Source code
convert.snpMatrix Man page Source code
convert.snpMatrix.dir Man page Source code
epsout.ld.snp Man page Source code
for.exercise Man page
forceHom Source code
genotype-class Man page
glm.test.control Man page Source code
guessSex Source code
haplotype-class Man page
ibs.stats Man page Source code
ibsCount Man page Source code
ibsDist Man page Source code
initialize,X.snp.matrix-method Man page
initialize,snp.matrix-method Man page
is.na,snp.matrix-method Man page
ld.snp Man page Source code
ld.with Man page Source code
ld.with,snp.matrix,character-method Man page
ld.with.internal Source code
ld.withmany Source code
niceprint Man page Source code
onLoad Source code
onUnload Source code
pair.result.ld.snp Man page Source code
plot.snp.dprime Man page Source code
print.snp.dprime Man page Source code
qq.chisq Man page Source code
rbind Man page
rbind,snp.matrix-method Man page
rbind2 Man page Source code
rbind2,snp.matrix,snp.matrix-method Man page
read.HapMap.data Man page Source code
read.pedfile.info Man page Source code
read.pedfile.map Man page Source code
read.snps.chiamo Man page Source code
read.snps.long Man page Source code
read.snps.long.old Man page Source code
read.snps.pedfile Man page Source code
read.wtccc.signals Man page Source code
row.summary Man page Source code
show,X.snp-method Man page
show,X.snp.matrix-method Man page
show,snp-method Man page
show,snp.matrix-method Man page
single.snp.tests Man page Source code
snp-class Man page
snp.cbind Man page Source code
snp.cor Man page Source code
snp.dprime-class Man page
snp.lhs.tests Man page Source code
snp.matrix-class Man page
snp.post Man page Source code
snp.pre Man page Source code
snp.rbind Man page Source code
snp.rhs.tests Man page Source code
snp.support Man page
snpMatrix Man page
snpMatrix-package Man page
snps.10 Man page
subject.data Man page
subject.support Man page
summary,X.snp.matrix-method Man page
summary,snp.matrix-method Man page
testdata Man page
write.snp.matrix Man page Source code
wtccc.sample.list Man page Source code
xxt Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/contingency.table.R
R/glm_test.R
R/ibs.stats.R
R/indata.R
R/ld.snp.R
R/ld.with.R
R/ld.with.R.eml.R
R/misc.R
R/outdata.R
R/qq_chisq.R
R/read.HapMap.R
R/read.chiamo.R
R/read.snps.pedfile.R
R/single.R
R/ss.R
R/structure.R
R/wtccc.sample.list.R
R/wtccc.signals.R
R/xstuff.R
R/zzz.R
build
build/vignette.rds
data
data/datalist
data/for.exercise.RData
data/testdata.RData
inst
inst/doc
inst/doc/chopsticks-vignette.R
inst/doc/chopsticks-vignette.Rnw
inst/doc/chopsticks-vignette.pdf
man
man/X.snp-class.Rd
man/X.snp.matrix-class.Rd
man/epsout.ld.snp.Rd
man/for.exercise.Rd
man/glm.test.control.Rd
man/ibs.stats.Rd
man/ibsCount.Rd
man/ibsDist.Rd
man/ld.snp.Rd
man/ld.with.Rd
man/pair.result.ld.snp.Rd
man/plot.snp.dprime.Rd
man/qq.chisq.Rd
man/read.HapMap.data.Rd
man/read.pedfile.info.Rd
man/read.pedfile.map.Rd
man/read.snps.chiamo.Rd
man/read.snps.long.Rd
man/read.snps.long.old.Rd
man/read.snps.pedfile.Rd
man/read.wtccc.signals.Rd
man/row.summary.Rd
man/single.snp.tests.Rd
man/snp-class.Rd
man/snp.cbind.Rd
man/snp.cor.Rd
man/snp.dprime-class.Rd
man/snp.lhs.tests.Rd
man/snp.matrix-class.Rd
man/snp.pre.Rd
man/snp.rhs.tests.Rd
man/snpMatrix-internal.Rd
man/snpMatrix-package.Rd
man/testdata.Rd
man/write.snp.matrix.Rd
man/wtccc.sample.list.Rd
man/xxt.Rd
src
src/Rmissing.h
src/adler32.c
src/bind.c
src/compress.c
src/crc32.c
src/crc32.h
src/deflate.c
src/deflate.h
src/force_hom.c
src/glm_test.c
src/glm_test.h
src/glm_test_R.c
src/gzio.c
src/hash_index.c
src/hash_index.h
src/ibs.c
src/in.c
src/infback.c
src/inffast.c
src/inffast.h
src/inffixed.h
src/inflate.c
src/inflate.h
src/inftrees.c
src/inftrees.h
src/input.c
src/inputNew.c
src/input_unsorted.c
src/ld_graphic_eps.c
src/ld_graphic_eps.h
src/ld_graphic_eps_priv.h
src/ld_with.c
src/mla.c
src/mla.h
src/outdata.c
src/pairwise_linkage.c
src/pairwise_linkage.h
src/read_chiamo.c
src/read_hapmap.c
src/read_pedfile.c
src/read_pedfile_priv.h
src/read_signals.c
src/read_tokens.h
src/readped.c
src/sdfpw.c
src/sdfpw.h
src/single_snp_tests.c
src/snp_summary.c
src/snpmpy.c
src/solve_cubic.c
src/solve_poly.h
src/solve_quadratic.c
src/structure.c
src/trees.c
src/trees.h
src/uncompr.c
src/zconf.h
src/zlib.h
src/zutil.c
src/zutil.h
vignettes
vignettes/CompatibilityMode.pdf
vignettes/chopsticks-vignette.Rnw
vignettes/index.html
vignettes/practical3_snpStatsBug-diff.pdf
vignettes/practical6_snpStatsBug-diff.pdf
vignettes/practical7_snpStatsBug-diff.pdf
vignettes/snpMatrix-4d.pdf
vignettes/snpMatrix-paper-HumanHeridity2007.pdf
vignettes/snpStatsBug-vignette.pdf
vignettes/snpStatsBug_1.3.6_-vignette.pdf
vignettes/snpStatsBug_1.5.4_-vignette.pdf
chopsticks documentation built on May 20, 2017, 9:14 p.m.