Overview | The bedMethyl format | RBedMethyl as a plug-and-play connector | Ingest a bedMethyl file | Subsetting example | Region-level summaries | Coercion to downstream classes | Session info
Package: RBedMethyl 1.1.1
Vasileios Lemonidis
RBedMethyl: Disk-backed Representation of ONT bedMethyl Files
Bioconductor-native infrastructure for handling large nanoporetech modkit bedMethyl pileup files from ONT data using HDF5Array and DelayedArray.
Authors:
RBedMethyl_1.1.1.tar.gz
RBedMethyl_1.1.1.zip(r-4.7)RBedMethyl_1.1.1.zip(r-4.6)RBedMethyl_1.1.1.zip(r-4.5)
RBedMethyl_1.1.1.tgz(r-4.6-any)RBedMethyl_1.1.1.tgz(r-4.5-any)
RBedMethyl_1.1.1.tar.gz(r-4.7-any)RBedMethyl_1.1.1.tar.gz(r-4.6-any)
RBedMethyl_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RBedMethyl/json (API)
| # Install 'RBedMethyl' in R: |
| install.packages('RBedMethyl', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cmg-ua/rbedmethyl/issues
On BioConductor:RBedMethyl-1.1.0(bioc 3.24)RBedMethyl-1.0.0(bioc 3.23)
dnamethylationdifferentialmethylationepigeneticsinfrastructuredataimportsoftware
Last updated from:27e08621a0. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 215 | ||
| linux-devel-x86_64 | OK | 324 | ||
| source / vignettes | OK | 288 | ||
| linux-release-x86_64 | OK | 389 | ||
| macos-release-arm64 | OK | 173 | ||
| macos-oldrel-arm64 | OK | 166 | ||
| windows-devel | OK | 218 | ||
| windows-release | OK | 204 | ||
| windows-oldrel | OK | 214 | ||
| wasm-release | OK | 192 |
Exports:bedMethylFieldsbetafilterByCoveragereadBedMethylsubsetBysubsetByChromosomessubsetByRegionsummarizeByRegion
Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomebsseqcigarilloclicodetoolscpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolsh5mreadHDF5ArrayhttrIRangesjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalesSeqinfosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysviridisLiteXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Subset rows | [,RBedMethyl,ANY,missing,missing-method [,RBedMethyl,missing,missing,missing-method [,RBedMethyl-method |
| List retrievable bedMethyl fields | bedMethylFields |
| Per-site methylation fraction | beta,RBedMethyl,missing-method beta,RBedMethyl-method |
| Filter by coverage | filterByCoverage filterByCoverage,RBedMethyl-method |
| RBedMethyl class | RBedMethyl-class |
| Read an ONT modkit bedMethyl file | readBedMethyl |
| Subset by assay predicate | subsetBy subsetBy,RBedMethyl-method |
| Subset by chromosomes | subsetByChromosomes subsetByChromosomes,RBedMethyl-method |
| Subset by region | subsetByRegion subsetByRegion,RBedMethyl,character,numeric,numeric-method subsetByRegion,RBedMethyl-method |
| Subset by GRanges | subsetByRegion,RBedMethyl,GRanges,missing,missing-method subsetByRegion,RBedMethyl,GRanges-method |
| Summarize by regions | summarizeByRegion summarizeByRegion,RBedMethyl-method |
