Package: ARRmNormalization 1.53.0
Jean-Philippe Fortin
ARRmNormalization: Adaptive Robust Regression normalization for Illumina methylation data
Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.
Authors:
ARRmNormalization_1.53.0.tar.gz
ARRmNormalization_1.53.0.zip(r-4.7)ARRmNormalization_1.53.0.zip(r-4.6)ARRmNormalization_1.53.0.zip(r-4.5)
ARRmNormalization_1.53.0.tgz(r-4.6-any)ARRmNormalization_1.53.0.tgz(r-4.5-any)
ARRmNormalization_1.53.0.tar.gz(r-4.7-any)ARRmNormalization_1.53.0.tar.gz(r-4.6-any)
ARRmNormalization_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ARRmNormalization/json (API)
| # Install 'ARRmNormalization' in R: |
| install.packages('ARRmNormalization', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- ProbesType - Probe Design information for the 450k methylation assay
On BioConductor:ARRmNormalization-1.53.0(bioc 3.24)ARRmNormalization-1.52.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dnamethylationtwochannelpreprocessingmicroarray
Last updated from:be3f824514. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 143 | ||
| linux-devel-x86_64 | NOTE | 172 | ||
| source / vignettes | OK | 168 | ||
| linux-release-x86_64 | NOTE | 170 | ||
| macos-release-arm64 | NOTE | 107 | ||
| macos-oldrel-arm64 | NOTE | 138 | ||
| windows-devel | NOTE | 113 | ||
| windows-release | NOTE | 109 | ||
| windows-oldrel | NOTE | 107 | ||
| wasm-release | OK | 110 |
Exports:getBackgroundgetCoefficientsgetDesignInfogetQuantilesnormalizeARRmpositionPlotsquantilePlots
Dependencies:ARRmData
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ARRm normalization for Illumina methylation data | ARRmNormalization-package ARRmNormalization |
| Estimate background intensity from the negative control probes | getBackground |
| Return the coefficients from the ARRm linear model | getCoefficients |
| Build the chip and position indices | getDesignInfo |
| Return the percentiles of a betaMatrix for each probe type | getQuantiles |
| Perform ARRm normalization | normalizeARRm |
| Plots to evalue chip position effects on different percentiles | positionPlots |
| Probe Design information for the 450k methylation assay | ProbesType |
| Diagnostic plots for evaluation of background effects and dye bias effects on different percentiles | quantilePlots |