Package: cpvSNP 1.39.0
Caitlin McHugh
cpvSNP: Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.
Authors:
cpvSNP_1.39.0.tar.gz
cpvSNP_1.39.0.zip(r-4.5)cpvSNP_1.39.0.zip(r-4.4)cpvSNP_1.39.0.zip(r-4.3)
cpvSNP_1.39.0.tgz(r-4.4-any)cpvSNP_1.39.0.tgz(r-4.3-any)
cpvSNP_1.39.0.tar.gz(r-4.5-noble)cpvSNP_1.39.0.tar.gz(r-4.4-noble)
cpvSNP_1.39.0.tgz(r-4.4-emscripten)cpvSNP_1.39.0.tgz(r-4.3-emscripten)
cpvSNP.pdf |cpvSNP.html✨
cpvSNP/json (API)
NEWS
| # Install 'cpvSNP' in R: |
| install.packages('cpvSNP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- geneSetAnalysis - Data to run gene set analysis methods
On BioConductor:cpvSNP-1.39.0(bioc 3.21)cpvSNP-1.38.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneticsstatisticalmethodpathwaysgenesetenrichmentgenomicvariation
Last updated 2 months agofrom:644afbbd19. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 03 2024 |
| R-4.5-win | NOTE | Dec 03 2024 |
| R-4.5-linux | NOTE | Dec 03 2024 |
| R-4.4-win | NOTE | Dec 03 2024 |
| R-4.4-mac | NOTE | Dec 03 2024 |
| R-4.3-win | NOTE | Dec 03 2024 |
| R-4.3-mac | NOTE | Dec 03 2024 |
Exports:assocPvalBySetPlotcreateArrayDatadegreesOfFreedomgeneSetNamegeneToSNPListglossiglossiMarginalplotPvalspValuesimulate_chisqsimulatedStatsstatisticvegasvegasMarginal
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscolorspacecorpcorcpp11crayoncurlDBIDelayedArrayfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegraphGSEABasegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create a Density Plot of P-Values, Highlighting SNPs Within a Gene Set | assocPvalBySetPlot |
| Create a GRanges Object for a GWAS data.frame | createArrayData |
| ~~ Methods for Function 'degreesOfFreedom' ~~ | degreesOfFreedom degreesOfFreedom,GeneSetResult-method degreesOfFreedom,GeneSetResultCollection-method degreesOfFreedom,GLOSSIResult-method degreesOfFreedom,GLOSSIResultCollection-method degreesOfFreedom,VEGASResult-method degreesOfFreedom,VEGASResultCollection-method degreesOfFreedom-methods |
| SNP Array Data to Use for Gene Set Analysis | exampleArrayData |
| Data to run gene set analysis methods | geneSetAnalysis |
| ~~ Methods for Function 'geneSetName' ~~ | geneSetName geneSetName,GeneSetResult-method geneSetName,GeneSetResultCollection-method geneSetName,GLOSSIResult-method geneSetName,GLOSSIResultCollection-method geneSetName,VEGASResult-method geneSetName,VEGASResultCollection-method geneSetName-methods |
| Class '"GeneSetResult"' | GeneSetResult-class |
| Class '"GeneSetResultCollection"' | GeneSetResultCollection-class |
| Gene Set Collection object | geneSets |
| Translate a List of Gene Ids to Their Corresponding SNP Ids | geneToSNPList |
| Calculate a Chi-squared Statistic and P-Value for Independent Items of a Set Using the GLOSSI Method | glossi |
| Calculate a Chi-squared Statistic and P-Value for Items in a Set | glossiMarginal |
| Class '"GLOSSIResult"' | GLOSSIResult-class |
| Class '"GLOSSIResultCollection"' | GLOSSIResultCollection-class |
| Create a Plot of P-Values Against Number of SNPs per Set for All Sets in a Collection | plotPvals |
| ~~ Methods for Function 'pValue' ~~ | pValue pValue,GeneSetResult-method pValue,GeneSetResultCollection-method pValue,GLOSSIResult-method pValue,GLOSSIResultCollection-method pValue,VEGASResult-method pValue,VEGASResultCollection-method pValue-methods |
| Simulate a Chi-squared Statistic from a Distribution with a Specified Correlation Structure | simulate_chisq |
| ~~ Methods for Function 'simulatedStats' ~~ | simulatedStats simulatedStats,VEGASResult-method simulatedStats,VEGASResultCollection-method simulatedStats-methods |
| ~~ Methods for Function 'statistic' ~~ | statistic statistic,GeneSetResult-method statistic,GeneSetResultCollection-method statistic,GLOSSIResult-method statistic,GLOSSIResultCollection-method statistic,VEGASResult-method statistic,VEGASResultCollection-method statistic-methods |
| ~~ Methods for Function 'show' in Package 'base' ~~ | show show,GLOSSIResult-method show,VEGASResult-method show-methods |
| Calculate the P-Value for a Set Using the VEGAS Method | vegas |
| Calculate the P-Value for a Set Using the VEGAS Method | vegasMarginal |
| Class '"VEGASResult"' | VEGASResult-class |
| Class '"VEGASResultCollection"' | VEGASResultCollection-class |
