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

Files in this package

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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