Installation | Bioconductor Installation | Development Version Installation | regionalpcs R Package Tutorial | Loading Required Packages | Load the Dataset | Loading Minfi Sample Dataset | Obtaining Methylation Array Probe Positions | Load Illumina 450k Array Probe Positions | Summarizing Gene Region Types | Introduction | Load Gene Region Annotations | Create a Region Map | Summarizing Gene Regions with Regional Principal Components | Compute Regional PCs | Inspecting the Output | Extracting and Viewing Regional PCs | Understanding the Results | Session Information
Package: regionalpcs 1.11.0
Tiffany Eulalio
regionalpcs: Summarizing Regional Methylation with Regional Principal Components Analysis
Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.
Authors:
regionalpcs_1.11.0.tar.gz
regionalpcs_1.11.0.zip(r-4.7)regionalpcs_1.11.0.zip(r-4.6)regionalpcs_1.11.0.zip(r-4.5)
regionalpcs_1.11.0.tgz(r-4.6-any)regionalpcs_1.11.0.tgz(r-4.5-any)
regionalpcs_1.11.0.tar.gz(r-4.7-any)regionalpcs_1.11.0.tar.gz(r-4.6-any)
regionalpcs_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
regionalpcs/json (API)
| # Install 'regionalpcs' in R: |
| install.packages('regionalpcs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tyeulalio/regionalpcs/issues
On BioConductor:regionalpcs-1.11.0(bioc 3.24)regionalpcs-1.10.0(bioc 3.23)
dnamethylationdifferentialmethylationstatisticalmethodsoftwaremethylationarray
Last updated from:15c6b22aeb. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 345 | ||
| linux-devel-x86_64 | OK | 397 | ||
| source / vignettes | OK | 421 | ||
| linux-release-x86_64 | OK | 379 | ||
| macos-release-arm64 | OK | 183 | ||
| macos-oldrel-arm64 | OK | 174 | ||
| windows-devel | OK | 1631 | ||
| windows-release | OK | 1634 | ||
| windows-oldrel | OK | 1593 | ||
| wasm-release | OK | 356 |
Exports:combine_resultscompute_dimensioncompute_regional_pcscreate_region_mapget_sig_pcssummarize_region
Dependencies:abindassortheadbeachmatBHBiocGenericsBiocParallelBiocSingularclicodetoolscowplotcpp11DelayedArrayDelayedMatrixStatsdplyrdqrngfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelgluegtableIRangesirlbaisobandlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsPCAtoolspillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangrsvdS4ArraysS4VectorsS7ScaledMatrixscalesSeqinfositmosnowSparseArraysparseMatrixStatsstringistringrtibbletidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Combine results dataframes across regions | combine_results |
| Compute significant dimensions of a matrix using the Marchenko-Pastur or Gavish-Donoho methods | compute_dimension |
| Compute regional principal components for methylation data | compute_regional_pcs |
| Create a Region Map Between CpGs and Gene Regions | create_region_map |
| Get significant principal components | get_sig_pcs |
| Summarize a region using regional principal components | summarize_region |
