Package: GenomicDataStream 0.99.28

Gabriel Hoffman

GenomicDataStream: Read Genomic Data Files (VCF, BCF, BGEN, PGEN, BED, H5AD) into R/Rcpp in Chunks

Read genomic data files (i.e. VCF, BCF, BGEN, PGEN, BED, H5AD, DelayedArray) into R/Rcpp in chunks for analysis with Armadillo / Eigen / Rcpp libraries. Modern datasets are often too big to fit into memory, and many analyses operate on a small chunk features at a time. GenomicDataStream provides interfaces at both the C++ and R levels for out-of-core analysis.

Authors:Gabriel Hoffman [aut, cre], Zilong Li [aut]

GenomicDataStream_0.99.28.tar.gz
GenomicDataStream_0.99.28.zip(r-4.7-x86_64)GenomicDataStream_0.99.28.zip(r-4.7-arm64)GenomicDataStream_0.99.28.zip(r-4.6-x86_64)GenomicDataStream_0.99.28.zip(r-4.6-arm64)GenomicDataStream_0.99.28.zip(r-4.5-x86_64)
GenomicDataStream_0.99.28.tgz(r-4.6-x86_64)GenomicDataStream_0.99.28.tgz(r-4.6-arm64)GenomicDataStream_0.99.28.tgz(r-4.5-x86_64)GenomicDataStream_0.99.28.tgz(r-4.5-arm64)
GenomicDataStream_0.99.28.tar.gz(r-4.7-arm64)GenomicDataStream_0.99.28.tar.gz(r-4.7-x86_64)GenomicDataStream_0.99.28.tar.gz(r-4.6-arm64)GenomicDataStream_0.99.28.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GenomicDataStream/json (API)

# Install 'GenomicDataStream' in R:
install.packages('GenomicDataStream', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gabrielhoffman/genomicdatastream/issues

Uses libs:
  • openblas– Optimized BLAS
  • zlib– Compression library
  • curl– Easy-to-use client-side URL transfer library
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

dataimportinfrastructureopenblaszlibcurlcpp

4.65 score 27 exports 60 dependencies

Last updated from:834e39c320. Checks:8 NOTE, 2 WARNING, 5 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE442
linux-devel-arm64WARNING483
linux-devel-x86_64WARNING548
source / vignettesOK714
linux-release-arm64NOTE479
linux-release-x86_64OK939
macos-release-arm64OK416
macos-release-x86_64NOTE720
macos-oldrel-arm64NOTE426
macos-oldrel-x86_64NOTE758
windows-devel-arm64OK562
windows-devel-x86_64NOTE694
windows-release-arm64OK597
windows-release-x86_64NOTE730
windows-oldrel-x86_64NOTE995
wasm-releaseFAIL203

Exports:.dashSVDatEndOfStreamchopChromscollapseRegionscountChunksdashSVDfeaturesReadGenomicDataStreamgetChromRangesgetNextChunkgetSampleNamesgetVariantLocationsinitializeStreamisInitializedmat_prod_AtAQnormPCPCAoneperfMetricplotprintreadH5ADrownamessetChunkSizesetRegionshowstandardize_in_placesummarizeChunks

Dependencies:abindanndataRassortheadbeachmatbeachmat.hdf5BHBiobaseBiocGenericsbiocmakecliDelayedArraydir.expirydplyrfilelockgenericsGenomicRangesglueh5mreadHDF5ArrayhereIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpngpurrrR6rappdirsRcppRcppArmadilloRcppEigenRcppParallelRcppTOMLreticulaterhdf5rhdf5filtersRhdf5librlangrprojrootS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimenttibbletidyselectutf8vcfppRvctrswithrXVector

Issues on Mac OS X
Install TBB using brew | Install RcppParallel with TBB path | Session info
Rendered frommac_osx.Rmdusingknitr::rmarkdown

Last update: 2026-09-10
Started: 2026-09-10

Extending GenomicDataStream
Additional file types | Additional matrix types | Importing into other projects
Rendered fromextensions.Rmdusingknitr::rmarkdown

Last update: 2025-10-28
Started: 2024-12-01

Reading data as a GenomicDataStream
Usage | Example code with R | Read genotype data into R | Use R to run analysis at C++ level | Example code with C++17 | Data types | Session info
Rendered fromGenomicDataStream.Rmdusingknitr::rmarkdown

Last update: 2025-10-28
Started: 2024-12-01

Readme and manuals

Help Manual

Help pageTopics
Detected if end of stream is reachedatEndOfStream
Get genomic intervalschopChroms
Get chunk sizescountChunks
Dynamic Shifts Based Randomized SVDdashSVD dashSVD,ANY-method
Get number of features read from GenomicDataStreamfeaturesRead
GenomicDataStreamGenomicDataStream
Interface to genomic data filesGenomicDataStream-class
Get ranges for each chromosomegetChromRanges
Get data chunk from GenomicDataStreamgetNextChunk
Get sample namesgetSampleNames
Get location of each featuregetVariantLocations
Initialize GenomicDataStreaminitializeStream
Get status of GenomicDataStreamisInitialized
Normalize principal componentsnormPC
PCA resultPCA-class
Window-based Randomized SVD with PCAonePCAone PCAone,GenomicDataStream-method
Evaluate performance of PC estimatesperfMetric
Plot PCAoneplot,PCA,ANY-method plot,PCA-method
Print objectprint,GenomicDataStream,GenomicDataStream-method print,GenomicDataStream-method print,PCA-method
Read H5AD as SingleCellExperimentreadH5AD
Get rownamesrownames,GenomicDataStream-method
Set Chunk SizesetChunkSize
Set regions of GenomicDataStreamsetRegion
Show objectshow,GenomicDataStream,GenomicDataStream-method show,GenomicDataStream-method show,PCA,PCA-method show,PCA-method
Standardize matrix columns in placestandardize_in_place
Get information about chunkssummarizeChunks