Package: preprocessCore 1.75.0
Ben Bolstad
preprocessCore: A collection of pre-processing functions
A library of core preprocessing routines.
Authors:
preprocessCore_1.75.0.tar.gz
preprocessCore_1.75.0.zip(r-4.7-x86_64)preprocessCore_1.75.0.zip(r-4.6-x86_64)preprocessCore_1.75.0.zip(r-4.5-x86_64)
preprocessCore_1.75.0.tgz(r-4.6-x86_64)preprocessCore_1.75.0.tgz(r-4.6-arm64)preprocessCore_1.75.0.tgz(r-4.5-x86_64)preprocessCore_1.75.0.tgz(r-4.5-arm64)
preprocessCore_1.75.0.tar.gz(r-4.7-arm64)preprocessCore_1.75.0.tar.gz(r-4.7-x86_64)preprocessCore_1.75.0.tar.gz(r-4.6-arm64)preprocessCore_1.75.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.75.0(bioc 3.24)preprocessCore-1.74.0(bioc 3.23)
Last updated from:4e5bfc285f. Checks:1 ERROR, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 159 | ||
| linux-devel-arm64 | WARNING | 124 | ||
| linux-devel-x86_64 | WARNING | 140 | ||
| source / vignettes | OK | 166 | ||
| linux-release-arm64 | WARNING | 125 | ||
| linux-release-x86_64 | WARNING | 184 | ||
| macos-release-arm64 | WARNING | 84 | ||
| macos-release-x86_64 | WARNING | 205 | ||
| macos-oldrel-arm64 | WARNING | 95 | ||
| macos-oldrel-x86_64 | WARNING | 194 | ||
| windows-devel-x86_64 | WARNING | 82 | ||
| windows-release-x86_64 | WARNING | 94 | ||
| windows-oldrel-x86_64 | WARNING | 86 | ||
| wasm-release | FAIL | 84 |
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 |
