snpStats: SnpMatrix and XSnpMatrix classes and methods

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

AuthorDavid Clayton <dc208@cam.ac.uk>
Date of publicationNone
MaintainerDavid Clayton <dc208@cam.ac.uk>
LicenseGPL-3
Version1.24.0

View on Bioconductor

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

Files

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

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