Package: stageR 1.33.0
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_1.33.0.tar.gz
stageR_1.33.0.zip(r-4.7)stageR_1.33.0.zip(r-4.6)stageR_1.33.0.zip(r-4.5)
stageR_1.33.0.tgz(r-4.6-any)stageR_1.33.0.tgz(r-4.5-any)
stageR_1.33.0.tar.gz(r-4.7-any)stageR_1.33.0.tar.gz(r-4.6-any)
stageR_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-1.33.0(bioc 3.24)stageR-1.34.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:d375191583. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 174 | ||
| linux-devel-x86_64 | WARNING | 288 | ||
| source / vignettes | ERROR | 279 | ||
| linux-release-x86_64 | WARNING | 269 | ||
| macos-release-arm64 | WARNING | 185 | ||
| macos-oldrel-arm64 | WARNING | 146 | ||
| windows-devel | WARNING | 249 | ||
| windows-release | WARNING | 264 | ||
| windows-oldrel | WARNING | 271 | ||
| wasm-release | OK | 150 |
Exports:adjustedAlphaLevelgetAdjustedPValuesgetAlphagetMethodgetPConfirmationgetPScreengetResultsgetSignificantGenesgetSignificantTxgetTx2geneisAdjustedisPScreenAdjustedstageRstageRTxstageWiseAdjustment
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
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 |
