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

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Implements classes and methods for large-scale SNP association studies

Author
Hin-Tak Leung <htl10@users.sourceforge.net>
Date of publication
None
Maintainer
Hin-Tak Leung <htl10@users.sourceforge.net>
License
GPL-3
Version
1.38.0
URLs

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