Package: snpStats 1.55.0
David Clayton
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.
Authors:
snpStats_1.55.0.tar.gz
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snpStats.pdf |snpStats.html✨
snpStats/json (API)
| # Install 'snpStats' in R: |
| install.packages('snpStats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- Asnps - Test data for the snpStats package
- Autosomes - Test data for the snpStats package
- Xchromosome - Test data for the snpStats package
- Xsnps - Test data for the snpStats package
- ceph.1mb - Datasets to illustrate calculation of linkage disequilibrium statistics
- genotypes - Test data for family association tests
- pedData - Test data for family association tests
- snp.support - Data for exercise in use of the snpStats package
- snps.10 - Data for exercise in use of the snpStats package
- subject.data - Test data for the snpStats package
- subject.support - Data for exercise in use of the snpStats package
- support.ld - Datasets to illustrate calculation of linkage disequilibrium statistics
- yri.1mb - Datasets to illustrate calculation of linkage disequilibrium statistics
On BioConductor:snpStats-1.55.0(bioc 3.20)snpStats-1.54.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:6be473e64c
Exports:can.imputecbindchi.squaredcoercecol.summaryconvert.snpMatrixconvert.snpMatrix.dirdeg.freedomeffect.signeffective.sample.sizefilter.rulesFstg2postglm.test.controlibsCountibsDistimputation.mafimputation.nsnpimputation.r2impute.snpsinitializeldmean2gmisinheritsmvtestsp.valueplotplotUncertaintypoolpool2post2gppqq.chisqrandom.snpsrbindread.beagleread.imputeread.longread.machread.pedfileread.plinkread.snps.longrow.summarysample.sizeshowsingle.snp.testssm.comparesnp.corsnp.imputationsnp.lhs.estimatessnp.lhs.testssnp.post.multiplysnp.pre.multiplysnp.rhs.estimatessnp.rhs.testssummaryswitch.allelestdt.snptest.allele.switchwrite.plinkwrite.SnpMatrixxxt
Dependencies:BiocGenericslatticeMatrixsurvivalzlibbioc
Data input
Rendered fromdata-input-vignette.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2015-08-14
Started: 2013-11-01
Fst
Rendered fromFst-vignette.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2022-07-27
Started: 2013-12-12
Imputation and meta-analysis
Rendered fromimputation-vignette.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2013-11-01
Started: 2013-11-01
LD statistics
Rendered fromld-vignette.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2013-11-01
Started: 2013-11-01
Principal components analysis
Rendered frompca-vignette.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2014-08-08
Started: 2013-11-01
snpMatrix-differences
Rendered fromdifferences.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2013-11-01
Started: 2013-11-01
snpStats introduction
Rendered fromsnpStats-vignette.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2013-11-01
Started: 2013-11-01
TDT tests
Rendered fromtdt-vignette.Rnwusingutils::Sweaveon Jul 03 2024.Last update: 2013-11-01
Started: 2013-11-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SnpMatrix and XSnpMatrix classes and methods | snpStats-package snpStats |
| Extract test statistics and p-values | chi.squared deg.freedom effect.sign effective.sample.size p.value sample.size |
| Convert 'snpMatrix' objects to 'snpStats' objects | convert.snpMatrix convert.snpMatrix.dir |
| An example of intensity data for SNP genotyping | example-new |
| Test data for family association tests | families genotypes pedData |
| Filter a set of imputation rules | filter.rules |
| Data for exercise in use of the snpStats package | for.exercise snp.support snps.10 subject.support |
| Calculate fixation indices | Fst |
| Set up control object for GLM computations | glm.test.control |
| Class "GlmEstimates" | coerce,GlmEstimates,GlmTests-method GlmEstimates-class show,GlmEstimates-method [,GlmEstimates,ANY,missing,missing-method |
| Classes "GlmTests" and "GlmTestsScore" | chi.squared,GlmTests,missing-method coerce,GlmTests,data.frame-method deg.freedom,GlmTests-method effect.sign,GlmTests,logical-method GlmTests-class GlmTestsScore-class names,GlmTests-method p.value,GlmTests,missing-method pool2,GlmTestsScore,GlmTestsScore,logical-method sample.size,GlmTests-method show,GlmTests-method summary,GlmTests-method switch.alleles,GlmTestsScore,character-method [,GlmTests,ANY,missing,missing-method [,GlmTestsScore,ANY,missing,missing-method |
| Count alleles identical by state | ibsCount |
| Distance matrix based on identity by state (IBS) | ibsDist |
| Extract statistics from imputation rules | can.impute imputation.maf imputation.nsnp imputation.r2 |
| Class "ImputationRules" | ImputationRules-class plot,ImputationRules,missing-method show,ImputationRules-method summary,ImputationRules-method [,ImputationRules,ANY,missing,missing-method |
| Impute snps | impute.snps |
| Pairwise linkage disequilibrium measures | ld |
| Datasets to illustrate calculation of linkage disequilibrium statistics | ceph.1mb ld.example support.ld yri.1mb |
| Raw coding of posterior probabilities of SNP genotype | g2post mean2g post2g |
| Find non-Mendelian inheritances in family data | misinherits |
| Multivariate SNP tests | mvtests |
| Plot posterior probabilities of genotype assignment | plotUncertainty |
| Pool test results from several studies or sub-studies | pool |
| Pool results of tests from two independent datasets | pool2 |
| Unpack posterior probabilities from one-byte codes | pp |
| Quantile-quantile plot for chi-squared tests | qq.chisq |
| Generate random SnpMatrix | random.snps |
| Read genotypes imputed by the BEAGLE program | read.beagle |
| Read genotypes imputed by the IMPUTE2 program | read.impute |
| Read SNP genotype data in long format | read.long |
| Read genotypes imputed by the MACH program | read.mach |
| Read a pedfile as '"SnpMatrix"' object | read.pedfile |
| Read a PLINK binary data file as a SnpMatrix | read.plink |
| Read SNP data in long format (deprecated) | read.snps.long |
| Summarize rows or columns of a snp matrix | col.summary row.summary |
| Sample datasets to illustrate data input | mach1.out.mlprob.gz sample-long-alleles.gz sample-long.gz sample.bed sample.bim sample.fam sample.info |
| 1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs) | single.snp.tests |
| Classes "SingleSnpTests" and "SingleSnpTestsScore" | chi.squared,SingleSnpTests,numeric-method coerce,SingleSnpTests,data.frame-method effect.sign,SingleSnpTestsScore,missing-method effective.sample.size,SingleSnpTests-method names,SingleSnpTests-method p.value,SingleSnpTests,numeric-method pool2,SingleSnpTestsScore,SingleSnpTestsScore,logical-method sample.size,SingleSnpTests-method show,SingleSnpTests-method SingleSnpTests-class SingleSnpTestsScore-class summary,SingleSnpTests-method switch.alleles,SingleSnpTestsScore,ANY-method [,SingleSnpTests,ANY,missing,missing-method [,SingleSnpTestsScore,ANY,missing,missing-method |
| Compare two SnpMatrix objects | sm.compare |
| Correlations with columns of a SnpMatrix | snp.cor |
| Calculate imputation rules | snp.imputation |
| Logistic regression with SNP genotypes as dependent variable | snp.lhs.estimates |
| Score tests with SNP genotypes as dependent variable | snp.lhs.tests |
| Pre- or post-multiply a SnpMatrix object by a general matrix | snp.post.multiply snp.pre.multiply |
| Fit GLMs with SNP genotypes as independent variable(s) | snp.rhs.estimates |
| Score tests with SNP genotypes as independent variable | snp.rhs.tests |
| Class "SnpMatrix" | cbind,SnpMatrix-method cbind2,SnpMatrix,SnpMatrix-method coerce,matrix,SnpMatrix-method coerce,SnpMatrix,character-method coerce,SnpMatrix,numeric-method initialize,SnpMatrix-method is.na,SnpMatrix-method rbind,SnpMatrix-method rbind2,SnpMatrix,SnpMatrix-method show,SnpMatrix-method SnpMatrix-class summary,SnpMatrix-method switch.alleles,SnpMatrix,ANY-method [,SnpMatrix,ANY,ANY,ANY-method |
| Switch alleles in columns of a SnpMatrix or in test results | switch.alleles |
| 1-df and 2-df tests for genetic associations with SNPs (or imputed SNPs) in family data | tdt.snp |
| Test for switch of alleles between two collections | test.allele.switch |
| Test data for the snpStats package | Asnps Autosomes subject.data testdata Xchromosome Xsnps |
| Write files for analysis in the PLINK toolset | write.plink |
| Write a SnpMatrix object as a text file | write.SnpMatrix |
| Class "XSnpMatrix" | coerce,SnpMatrix,XSnpMatrix-method coerce,XSnpMatrix,character-method initialize,XSnpMatrix-method show,XSnpMatrix-method summary,XSnpMatrix-method XSnpMatrix-class [,XSnpMatrix,ANY,ANY,ANY-method [<-,XSnpMatrix,ANY,ANY,XSnpMatrix-method |
| X.X-transpose for a standardized SnpMatrix | xxt |
