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

Files in this package

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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