Package: stageR 1.29.0
Koen Van den Berge
stageR: stageR: stage-wise analysis of high throughput gene expression data in R
The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is published in Genome Biology at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0
Authors:
stageR_1.29.0.tar.gz
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stageR.pdf |stageR.html✨
stageR/json (API)
| # Install 'stageR' in R: |
| install.packages('stageR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- esetProstate - Transcript-level abundance estimates in 14 Chinese prostate cancer patients
- hammer.eset - Hammer dataset
On BioConductor:stageR-1.29.0(bioc 3.21)stageR-1.28.0(bioc 3.20)
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:2a767cf78b. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | WARNING | Nov 30 2024 |
| R-4.5-linux | WARNING | Nov 30 2024 |
| R-4.4-win | WARNING | Nov 30 2024 |
| R-4.4-mac | WARNING | Nov 30 2024 |
| R-4.3-win | WARNING | Nov 30 2024 |
| R-4.3-mac | WARNING | Nov 30 2024 |
Exports:adjustedAlphaLevelgetAdjustedPValuesgetAlphagetMethodgetPConfirmationgetPScreengetResultsgetSignificantGenesgetSignificantTxgetTx2geneisAdjustedisPScreenAdjustedstageRstageRTxstageWiseAdjustment
Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get adjusted significance level from the screening stage. | adjustedAlphaLevel adjustedAlphaLevel,stageR adjustedAlphaLevel,stageRTx adjustedAlphaLevel,stageRTx-method |
| Transcript-level abundance estimates in 14 Chinese prostate cancer patients | esetProstate |
| Retrieve the stage-wise adjusted p-values. | getAdjustedPValues getAdjustedPValues,stageR getAdjustedPValues,stageRTx getAdjustedPValues,stageRTx,logical,logical-method |
| Retrieve the significance level for the stage-wise adjustment. | getAlpha getAlpha,stageR getAlpha,stageRTx getAlpha,stageRTx-method |
| Retrieve FWER correction method. | getMethod getMethod,stageR getMethod,stageRTx getMethod,stageRTx-method |
| Return unadjusted confirmation hypothesis p-values from a 'stageRClass' object. | getPConfirmation getPConfirmation,stageR getPConfirmation,stageRTx getPConfirmation,stageRTx-method |
| Return screening hypothesis p-values from a 'stageRClass' object. | getPScreen getPScreen,stageR getPScreen,stageRTx getPScreen,stageRTx-method |
| Get significance results according to a stage-wise analysis. | getResults getResults,stageR getResults,stageRTx |
| Return significant genes when performing transcript-level analysis. | getSignificantGenes getSignificantGenes,stageRTx |
| Return significant transcripts when performing transcript-level analysis. | getSignificantTx getSignificantTx,stageR getSignificantTx,stageRTx |
| Retrieve the data frame linking genes to transcripts. | getTx2gene getTx2gene,stageRTx |
| Hammer dataset | hammer.eset |
| Has stage-wise adjustment already been performed on the object? | isAdjusted isAdjusted,stageR isAdjusted,stageRTx isAdjusted,stageRTx-method |
| Are the screening p-values adjusted for multiplicity? | isPScreenAdjusted isPScreenAdjusted,stageR isPSCreenAdjusted,stageRTx isPScreenAdjusted,stageRTx-method |
| Create stageR object | stageR |
| The stageR class | stageRClass stageRTxClass |
| Create stageRTx object. | stageRTx |
| adjust p-values in a two-stage analysis | stageWiseAdjustment stageWiseAdjustment,stageR stageWiseAdjustment,stageRTx stageWiseAdjustment,stageRTx,character,numeric-method |
