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

Implements classes and methods for large-scale SNP association studies

AuthorHin-Tak Leung <htl10@users.sourceforge.net>
Date of publicationNone
MaintainerHin-Tak Leung <htl10@users.sourceforge.net>
LicenseGPL-3
Version1.38.0
http://outmodedbonsai.sourceforge.net/

View on Bioconductor

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

Files

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

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