Package: regionalpcs 1.5.0
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_1.5.0.tar.gz
regionalpcs_1.5.0.zip(r-4.5)regionalpcs_1.5.0.zip(r-4.4)regionalpcs_1.5.0.zip(r-4.3)
regionalpcs_1.5.0.tgz(r-4.4-any)regionalpcs_1.5.0.tgz(r-4.3-any)
regionalpcs_1.5.0.tar.gz(r-4.5-noble)regionalpcs_1.5.0.tar.gz(r-4.4-noble)
regionalpcs_1.5.0.tgz(r-4.4-emscripten)regionalpcs_1.5.0.tgz(r-4.3-emscripten)
regionalpcs.pdf |regionalpcs.html✨
regionalpcs/json (API)
NEWS
| # 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-1.5.0(bioc 3.21)regionalpcs-1.4.0(bioc 3.20)
dnamethylationdifferentialmethylationstatisticalmethodsoftwaremethylationarray
Last updated 2 months agofrom:78178d2ca5. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | OK | Nov 30 2024 |
| R-4.5-linux | OK | Nov 30 2024 |
| R-4.4-win | OK | Nov 30 2024 |
| R-4.4-mac | OK | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:combine_resultscompute_dimensioncompute_regional_pcscreate_region_mapget_sig_pcssummarize_region
Dependencies:abindaskpassassortheadbeachmatBHBiocGenericsBiocParallelBiocSingularclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayDelayedMatrixStatsdplyrdqrngfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehttrIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslPCAtoolspillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangrsvdS4ArraysS4VectorsScaledMatrixscalessitmosnowSparseArraysparseMatrixStatsstringistringrsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
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 |
