Package: preprocessCore 1.69.0
Ben Bolstad
preprocessCore: A collection of pre-processing functions
A library of core preprocessing routines.
Authors:
preprocessCore_1.69.0.tar.gz
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preprocessCore.pdf |preprocessCore.html✨
preprocessCore/json (API)
| # Install 'preprocessCore' in R: |
| install.packages('preprocessCore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bmbolstad/preprocesscore/issues
On BioConductor:preprocessCore-1.69.0(bioc 3.21)preprocessCore-1.68.0(bioc 3.20)
Last updated 4 months agofrom:d2e67f1e83. Checks:1 OK, 1 ERROR, 9 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 28 2025 |
| R-4.5-win-x86_64 | WARNING | Feb 28 2025 |
| R-4.5-mac-x86_64 | WARNING | Feb 28 2025 |
| R-4.5-mac-aarch64 | WARNING | Feb 28 2025 |
| R-4.5-linux-x86_64 | ERROR | Feb 28 2025 |
| R-4.4-win-x86_64 | WARNING | Feb 28 2025 |
| R-4.4-mac-x86_64 | WARNING | Feb 28 2025 |
| R-4.4-mac-aarch64 | WARNING | Feb 28 2025 |
| R-4.3-win-x86_64 | WARNING | Feb 28 2025 |
| R-4.3-mac-x86_64 | WARNING | Feb 28 2025 |
| R-4.3-mac-aarch64 | WARNING | Feb 28 2025 |
Exports:colSummarizeAvgcolSummarizeAvgLogcolSummarizeBiweightcolSummarizeBiweightLogcolSummarizeLogAvgcolSummarizeLogMediancolSummarizeMediancolSummarizeMedianLogcolSummarizeMedianpolishcolSummarizeMedianpolishLogconvert.group.labelsnormalize.quantilesnormalize.quantiles.determine.targetnormalize.quantiles.in.blocksnormalize.quantiles.robustnormalize.quantiles.use.targetrcModelMedianPolishrcModelPLMrcModelPLMdrcModelPLMrrcModelPLMrcrcModelPLMrrrcModelWPLMrcModelWPLMrrcModelWPLMrcrcModelWPLMrrrma.background.correctsubColSummarizeAvgsubColSummarizeAvgLogsubColSummarizeBiweightsubColSummarizeBiweightLogsubColSummarizeLogAvgsubColSummarizeLogMediansubColSummarizeMediansubColSummarizeMedianLogsubColSummarizeMedianpolishsubColSummarizeMedianpolishLogsubrcModelMedianPolishsubrcModelPLM
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Summarize the column of matrices | colSummarizeAvg colSummarizeAvgLog colSummarizeBiweight colSummarizeBiweightLog colSummarizeLogAvg colSummarizeLogMedian colSummarizeMedian colSummarizeMedianLog colSummarizeMedianpolish colSummarizeMedianpolishLog |
| Quantile Normalization | normalize.quantiles |
| Quantile Normalization carried out separately within blocks of rows | normalize.quantiles.in.blocks |
| Robust Quantile Normalization | normalize.AffyBatch.quantiles.robust normalize.quantiles.robust |
| Quantile Normalization using a specified target distribution vector | normalize.quantiles.determine.target normalize.quantiles.use.target |
| Fit robust row-column models to a matrix | rcModelPLMd |
| Fit robust row-column models to a matrix | rcModelPLMr rcModelPLMrc rcModelPLMrr rcModelWPLMr rcModelWPLMrc rcModelWPLMrr |
| Fit row-column model to a matrix | rcModelMedianPolish rcModelPLM rcModelWPLM |
| RMA Background Correction | rma.background.correct |
| Summarize columns when divided into groups of rows | convert.group.labels subColSummarizeAvg subColSummarizeAvgLog subColSummarizeBiweight subColSummarizeBiweightLog subColSummarizeLogAvg subColSummarizeLogMedian subColSummarizeMedian subColSummarizeMedianLog subColSummarizeMedianpolish subColSummarizeMedianpolishLog |
| Fit row-column model to a matrix | subrcModelMedianPolish subrcModelPLM subrcModelWPLM |
