snpStats: SnpMatrix and XSnpMatrix classes and methods

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

Author
David Clayton <dc208@cam.ac.uk>
Date of publication
None
Maintainer
David Clayton <dc208@cam.ac.uk>
License
GPL-3
Version
1.24.0

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
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("snpStats")}
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