snpStats: SnpMatrix and XSnpMatrix classes and methods
Version 1.26.0

Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

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AuthorDavid Clayton <dc208@cam.ac.uk>
Bioconductor views GeneticVariability Microarray SNP
Date of publicationNone
MaintainerDavid Clayton <dc208@cam.ac.uk>
LicenseGPL-3
Version1.26.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("snpStats")

Man pages

chi.squared: Extract test statistics and p-values
convert.snpMatrix: Convert 'snpMatrix' objects to 'snpStats' objects
example-new: An example of intensity data for SNP genotyping
families: Test data for family association tests
filter.rules: Filter a set of imputation rules
for.exercise: Data for exercise in use of the snpStats package
Fst: Calculate fixation indices
GlmEstimates-class: Class "GlmEstimates"
glm.test.control: Set up control object for GLM computations
GlmTests-class: Classes "GlmTests" and "GlmTestsScore"
ibsCount: Count alleles identical by state
ibsDist: Distance matrix based on identity by state (IBS)
imputation.maf: Extract statistics from imputation rules
ImputationRules-class: Class "ImputationRules"
impute.snps: Impute snps
ld: Pairwise linkage disequilibrium measures
ld.example: Datasets to illustrate calculation of linkage disequilibrium...
mean2g: Raw coding of posterior probabilities of SNP genotype
misinherits: Find non-Mendelian inheritances in family data
mvtests: Multivariate SNP tests
plotUncertainty: Plot posterior probabilities of genotype assignment
pool: Pool test results from several studies or sub-studies
pool2: Pool results of tests from two independent datasets
pp: Unpack posterior probabilities from one-byte codes
qq.chisq: Quantile-quantile plot for chi-squared tests
random.snps: Generate random SnpMatrix
read.beagle: Read genotypes imputed by the BEAGLE program
read.impute: Read genotypes imputed by the IMPUTE2 program
read.long: Read SNP genotype data in long format
read.mach: Read genotypes imputed by the MACH program
read.pedfile: Read a pedfile as '"SnpMatrix"' object
read.plink: Read a PLINK binary data file as a SnpMatrix
read.snps.long: Read SNP data in long format (deprecated)
row.summary: Summarize rows or columns of a snp matrix
sample: Sample datasets to illustrate data input
single.snp.tests: 1-df and 2-df tests for genetic associations with SNPs (or...
SingleSnpTests-class: Classes "SingleSnpTests" and "SingleSnpTestsScore"
sm.compare: Compare two SnpMatrix objects
snp.cor: Correlations with columns of a SnpMatrix
snp.imputation: Calculate imputation rules
snp.lhs.estimates: Logistic regression with SNP genotypes as dependent variable
snp.lhs.tests: Score tests with SNP genotypes as dependent variable
SnpMatrix-class: Class "SnpMatrix"
snp.pre.multiply: Pre- or post-multiply a SnpMatrix object by a general matrix
snp.rhs.estimates: Fit GLMs with SNP genotypes as independent variable(s)
snp.rhs.tests: Score tests with SNP genotypes as independent variable
snpStats-package: SnpMatrix and XSnpMatrix classes and methods
switch.alleles: Switch alleles in columns of a SnpMatrix or in test results
tdt.snp: 1-df and 2-df tests for genetic associations with SNPs (or...
test.allele.switch: Test for switch of alleles between two collections
testdata: Test data for the snpStats package
write.plink: Write files for analysis in the PLINK toolset
write.snp.matrix: Write a SnpMatrix object as a text file
XSnpMatrix-class: Class "XSnpMatrix"
xxt: X.X-transpose for a standardized SnpMatrix

Functions

Asnps Man page
Autosomes Man page
Fst Man page Source code
GlmEstimates-class Man page
GlmTests-class Man page
GlmTestsScore-class Man page
ImputationRules-class Man page
SingleSnpTests-class Man page
SingleSnpTestsScore-class Man page
SnpMatrix-class Man page
XSnpMatrix-class Man page
Xchromosome Man page
Xsnps Man page
[,GlmEstimates,ANY,missing,missing-method Man page
[,GlmTests,ANY,missing,missing-method Man page
[,GlmTestsScore,ANY,missing,missing-method Man page
[,ImputationRules,ANY,missing,missing-method Man page
[,SingleSnpTests,ANY,missing,missing-method Man page
[,SingleSnpTestsScore,ANY,missing,missing-method Man page
[,SnpMatrix,ANY,ANY,ANY-method Man page
[,XSnpMatrix,ANY,ANY,ANY-method Man page
[<-,XSnpMatrix,ANY,ANY,XSnpMatrix-method Man page
can.impute Man page Source code
cbind,SnpMatrix-method Man page
cbind2,SnpMatrix,SnpMatrix-method Man page
ceph.1mb Man page
chi.squared Man page
chi.squared,GlmTests,missing-method Man page
chi.squared,SingleSnpTests,numeric-method Man page
coerce,GlmEstimates,GlmTests-method Man page
coerce,GlmTests,data.frame-method Man page
coerce,SingleSnpTests,data.frame-method Man page
coerce,SnpMatrix,XSnpMatrix-method Man page
coerce,SnpMatrix,character-method Man page
coerce,SnpMatrix,numeric-method Man page
coerce,XSnpMatrix,character-method Man page
coerce,matrix,SnpMatrix-method Man page
col.numbers Source code
col.summary Man page Source code
contingency.table Source code
convert.snpMatrix Man page Source code
convert.snpMatrix.dir Man page Source code
deg.freedom Man page
deg.freedom,GlmTests-method Man page
effect.sign Man page
effect.sign,GlmTests,logical-method Man page
effect.sign,SingleSnpTestsScore,missing-method Man page
effective.sample.size Man page
effective.sample.size,SingleSnpTests-method Man page
example-new Man page
families Man page
filter.rules Man page Source code
for.exercise Man page
forceHom Source code
g2post Man page Source code
genotypes Man page
glm.test.control Man page Source code
guessPloidy Source code
ibsCount Man page Source code
ibsDist Man page Source code
imputation.maf Man page Source code
imputation.nsnp Man page Source code
imputation.r2 Man page Source code
impute.snps Man page Source code
initialize,SnpMatrix-method Man page
initialize,XSnpMatrix-method Man page
is.na,SnpMatrix-method Man page
ld Man page Source code
ld.example Man page
mach1.out.mlprob.gz Man page
mean2g Man page Source code
misinherits Man page Source code
mvtests Man page Source code
names,GlmTests-method Man page
names,SingleSnpTests-method Man page
p.value Man page
p.value,GlmTests,missing-method Man page
p.value,SingleSnpTests,numeric-method Man page
pedData Man page
plot,ImputationRules,missing-method Man page
plotUncertainty Man page Source code
pool Man page Source code
pool2 Man page
pool2,GlmTestsScore,GlmTestsScore,logical-method Man page
pool2,SingleSnpTestsScore,SingleSnpTestsScore,logical-method Man page
post2g Man page Source code
pp Man page Source code
qq.chisq Man page Source code
random.snps Man page Source code
rbind,SnpMatrix-method Man page
rbind2,SnpMatrix,SnpMatrix-method Man page
read.beagle Man page Source code
read.impute Man page Source code
read.long Man page Source code
read.mach Man page Source code
read.pedfile Man page Source code
read.plink Man page Source code
read.snps.long Man page Source code
row.summary Man page Source code
sample-long-alleles.gz Man page
sample-long.gz Man page
sample.bed Man page
sample.bim Man page
sample.fam Man page
sample.info Man page
sample.size Man page
sample.size,GlmTests-method Man page
sample.size,SingleSnpTests-method Man page
show,GlmEstimates-method Man page
show,GlmTests-method Man page
show,ImputationRules-method Man page
show,SingleSnpTests-method Man page
show,SnpMatrix-method Man page
show,XSnpMatrix-method Man page
single.snp.tests Man page Source code
sm.compare Man page Source code
snp.cbind Source code
snp.cor Man page Source code
snp.imputation Man page Source code
snp.lhs.estimates Man page Source code
snp.lhs.tests Man page Source code
snp.post.multiply Man page Source code
snp.pre.multiply Man page Source code
snp.rbind Source code
snp.rhs.estimates Man page Source code
snp.rhs.tests Man page Source code
snp.support Man page
snpStats Man page
snpStats-package Man page
snps.10 Man page
subject.data Man page
subject.support Man page
summary,GlmTests-method Man page
summary,ImputationRules-method Man page
summary,SingleSnpTests-method Man page
summary,SnpMatrix-method Man page
summary,XSnpMatrix-method Man page
support.ld Man page
switch.alleles Man page
switch.alleles,GlmTestsScore,character-method Man page
switch.alleles,SingleSnpTestsScore,ANY-method Man page
switch.alleles,SnpMatrix,ANY-method Man page
tdt.snp Man page Source code
test.allele.switch Man page Source code
testdata Man page
write.SnpMatrix Man page Source code
write.plink Man page Source code
xxt Man page Source code
yri.1mb Man page

Files

DESCRIPTION
NAMESPACE
R
R/compare.R
R/contingency.table.R
R/convert.R
R/glm-test.R
R/imputation.R
R/indata.R
R/ld.R
R/long.R
R/misc.R
R/mvtests.R
R/outdata.R
R/pedfile.R
R/plink.R
R/qc.R
R/qq-chisq.R
R/single.R
R/ss.R
R/structure.R
R/tdt-single.R
R/xstuff.R
build
build/partial.rdb
build/vignette.rds
data
data/datalist
data/families.RData
data/for.exercise.RData
data/ld.example.RData
data/testdata.RData
inst
inst/doc
inst/doc/Fst-vignette.R
inst/doc/Fst-vignette.Rnw
inst/doc/Fst-vignette.pdf
inst/doc/data-input-vignette.R
inst/doc/data-input-vignette.Rnw
inst/doc/data-input-vignette.pdf
inst/doc/differences.Rnw
inst/doc/differences.pdf
inst/doc/imputation-vignette.R
inst/doc/imputation-vignette.Rnw
inst/doc/imputation-vignette.pdf
inst/doc/ld-vignette.R
inst/doc/ld-vignette.Rnw
inst/doc/ld-vignette.pdf
inst/doc/pca-vignette.R
inst/doc/pca-vignette.Rnw
inst/doc/pca-vignette.pdf
inst/doc/snpStats-vignette.R
inst/doc/snpStats-vignette.Rnw
inst/doc/snpStats-vignette.pdf
inst/doc/tdt-vignette.R
inst/doc/tdt-vignette.Rnw
inst/doc/tdt-vignette.pdf
inst/extdata
inst/extdata/mach1.out.mlprob.gz
inst/extdata/sample-long-alleles.gz
inst/extdata/sample-long.gz
inst/extdata/sample.bed
inst/extdata/sample.bim
inst/extdata/sample.fam
inst/extdata/sample.info
inst/extdata/sample.ped.gz
man
man/Fst.Rd
man/GlmEstimates-class.Rd
man/GlmTests-class.Rd
man/ImputationRules-class.Rd
man/SingleSnpTests-class.Rd
man/SnpMatrix-class.Rd
man/XSnpMatrix-class.Rd
man/chi.squared.Rd
man/convert.snpMatrix.Rd
man/example-new.Rd
man/families.Rd
man/filter.rules.Rd
man/for.exercise.Rd
man/glm.test.control.Rd
man/ibsCount.Rd
man/ibsDist.Rd
man/imputation.maf.Rd
man/impute.snps.Rd
man/ld.Rd
man/ld.example.Rd
man/mean2g.Rd
man/misinherits.Rd
man/mvtests.Rd
man/plotUncertainty.Rd
man/pool.Rd
man/pool2.Rd
man/pp.Rd
man/qq.chisq.Rd
man/random.snps.Rd
man/read.beagle.Rd
man/read.impute.Rd
man/read.long.Rd
man/read.mach.Rd
man/read.pedfile.Rd
man/read.plink.Rd
man/read.snps.long.Rd
man/row.summary.Rd
man/sample.Rd
man/single.snp.tests.Rd
man/sm.compare.Rd
man/snp.cor.Rd
man/snp.imputation.Rd
man/snp.lhs.estimates.Rd
man/snp.lhs.tests.Rd
man/snp.pre.multiply.Rd
man/snp.rhs.estimates.Rd
man/snp.rhs.tests.Rd
man/snpStats-package.Rd
man/switch.alleles.Rd
man/tdt.snp.Rd
man/test.allele.switch.Rd
man/testdata.Rd
man/write.plink.Rd
man/write.snp.matrix.Rd
man/xxt.Rd
src
src/Makevars
src/Makevars.win
src/Rmissing.h
src/Runcertain.c
src/bind.c
src/count_gt.c
src/covwin.c
src/covwin.h
src/crc32.h
src/deflate.h
src/force_hom.c
src/fst.c
src/glm_test.c
src/glm_test.h
src/glm_test_R.c
src/gsl_poly.h
src/hash_index.c
src/hash_index.h
src/hphase.c
src/hphase.h
src/imputation.c
src/imputation.h
src/in.c
src/inffast.h
src/inffixed.h
src/inflate.h
src/inftrees.h
src/input.c
src/invert.c
src/invert.h
src/ipf.c
src/ipf.h
src/ld.c
src/misc.c
src/mla.c
src/mla.h
src/mvphenotype.c
src/outdata.c
src/plink.c
src/read_uncertain.c
src/readped.c
src/single_snp_tests.c
src/snp_summary.c
src/snpmpy.c
src/solve_cubic.c
src/structure.c
src/subset.c
src/switch.c
src/tdt.c
src/testBig.c
src/uncertain.c
src/uncertain.h
vignettes
vignettes/Fst-vignette.Rnw
vignettes/data-input-vignette.Rnw
vignettes/differences.Rnw
vignettes/imputation-vignette.Rnw
vignettes/index.html
vignettes/ld-vignette.Rnw
vignettes/pca-vignette.Rnw
vignettes/snpStats-vignette.Rnw
vignettes/tdt-vignette.Rnw
snpStats documentation built on May 20, 2017, 10:01 p.m.