Introduction | Quick Start | Overview of classes and functions | GenomicFiles class | Functions | Queries across files: reduceByRange and reduceRanges | Pileup summaries | Basepair-level $t$-test with case / control groups | Queries within files: reduceByFile and reduceFiles | Counting read junctions | Coverage 1: reduceByFile | Coverage 2: reduceFiles | Coverage 3: reduceFiles with chunking | Chunking | Ranges in a file | Records in a file | sessionInfo()
Package: GenomicFiles 1.49.0
Bioconductor Package Maintainer
GenomicFiles: Distributed computing by file or by range
This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.
Authors:
GenomicFiles_1.49.0.tar.gz
GenomicFiles_1.49.0.zip(r-4.7)GenomicFiles_1.49.0.zip(r-4.6)GenomicFiles_1.49.0.zip(r-4.5)
GenomicFiles_1.49.0.tgz(r-4.6-any)GenomicFiles_1.49.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GenomicFiles/json (API)
| # Install 'GenomicFiles' in R: |
| install.packages('GenomicFiles', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/genomicfiles/issues
On BioConductor:GenomicFiles-1.49.0(bioc 3.24)GenomicFiles-1.48.0(bioc 3.23)
geneticsinfrastructuredataimportsequencingcoveragebioconductor-packagecore-packageu24ca289073
Last updated from:f260700483. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 274 | ||
| linux-devel-x86_64 | OK | 571 | ||
| source / vignettes | OK | 444 | ||
| linux-release-x86_64 | OK | 561 | ||
| macos-release-arm64 | OK | 284 | ||
| macos-oldrel-arm64 | OK | 270 | ||
| windows-devel | OK | 874 | ||
| windows-release | OK | 870 | ||
| windows-oldrel | OK | 846 | ||
| wasm-release | OK | 216 |
Exports:.fileTypeRegistryassaycolDatacolData<-colnamescountBamcoveragefilesfiles<-findTypeRegistryGenomicFilesgetVCFPathmakeFileTypepackpaths1kgRangedVcfStackreadVcfStackreduceByFilereduceByRangereduceByYieldreduceFilesreduceRangesREDUCEsamplerregisterFileTyperownamesrowRangesrowRanges<-scanBamseqinfoseqinfo<-showsummarizeOverlapssummaryunpackvcfFieldsVcfStackyieldSize
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GenomicFiles objects | class:GenomicFiles colData<-,GenomicFiles,DataFrame-method dimnames<-,GenomicFiles,list-method files files,GenomicFiles-method files<- files<-,GenomicFiles,character-method files<-,GenomicFiles,List-method GenomicFiles GenomicFiles,GenomicRanges_OR_GRangesList,character-method GenomicFiles,GenomicRanges_OR_GRangesList,List-method GenomicFiles,GenomicRanges_OR_GRangesList,list-method GenomicFiles,missing,ANY-method GenomicFiles,missing,missing-method GenomicFiles-class show,GenomicFiles-method [,GenomicFiles,ANY,ANY,ANY-method [,GenomicFiles,ANY,ANY-method |
| Deprecated functions in package 'GenomicFiles' | GenomicFiles-deprecated getVCFPath |
| Range transformations of a 'GenomicRanges' object for optimal file queries. | isPacked pack pack,GRanges-method |
| Parallel computations by files | reduceByFile reduceByFile,GenomicFiles,missing-method reduceByFile,GRanges,ANY-method reduceByFile,GRangesList,ANY-method reduceFiles |
| Parallel computations by ranges | reduceByRange reduceByRange,GenomicFiles,missing-method reduceByRange,GRanges,ANY-method reduceByRange,GRangesList,ANY-method reduceRanges |
| Iterate through a BAM (or other) file, reducing output to a single result. | reduceByYield REDUCEsampler |
| Functions for creating and searching a registry of file types. | findTypeRegistry makeFileType registerFileType registry-utils |
| Un-pack results obtained with a pack()ed group of ranges | unpack unpack,List,GRangesList-method unpack,list,GRangesList-method |
| VcfStack and RangedVcfStack Objects | assay,RangedVcfStack,ANY-method assay,VcfStack,ANY-method class:VcfStack colData,VcfStack-method colData<-,VcfStack,DataFrame-method colnames,VcfStack-method dim,VcfStack-method dimnames,VcfStack-method files,VcfStack-method files<-,VcfStack,character-method files<-,VcfStack,VcfFile-method files<-,VcfStack,VcfFileList-method paths1kg RangedVcfStack RangedVcfStack-class readVcfStack rownames,VcfStack-method rowRanges,RangedVcfStack-method rowRanges<-,RangedVcfStack,GRanges-method seqinfo,VcfStack-method seqinfo<-,RangedVcfStack-method seqinfo<-,VcfStack-method seqlevelsStyle<-,RangedVcfStack-method seqlevelsStyle<-,VcfStack-method show,VcfStack-method vcfFields,VcfStack-method VcfStack VcfStack-class [,RangedVcfStack,ANY,ANY,ANY-method [,RangedVcfStack,ANY,ANY-method [,VcfStack,ANY,ANY,ANY-method [,VcfStack,ANY,ANY-method |
