Package: VariantExperiment 1.21.0
Qian Liu
VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.
Authors:
VariantExperiment_1.21.0.tar.gz
VariantExperiment_1.21.0.zip(r-4.5)VariantExperiment_1.21.0.zip(r-4.4)VariantExperiment_1.21.0.zip(r-4.3)
VariantExperiment_1.21.0.tgz(r-4.4-any)VariantExperiment_1.21.0.tgz(r-4.3-any)
VariantExperiment_1.21.0.tar.gz(r-4.5-noble)VariantExperiment_1.21.0.tar.gz(r-4.4-noble)
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VariantExperiment.pdf |VariantExperiment.html✨
VariantExperiment/json (API)
NEWS
| # Install 'VariantExperiment' in R: |
| install.packages('VariantExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/variantexperiment/issues
On BioConductor:VariantExperiment-1.21.0(bioc 3.21)VariantExperiment-1.20.0(bioc 3.20)
infrastructuredatarepresentationsequencingannotationgenomeannotationgenotypingarray
Last updated 23 days agofrom:f3af19ff6f. Checks:OK: 1 NOTE: 1 ERROR: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | ERROR | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | ERROR | Oct 31 2024 |
| R-4.4-mac | ERROR | Oct 31 2024 |
| R-4.3-win | ERROR | Oct 31 2024 |
| R-4.3-mac | ERROR | Oct 31 2024 |
Exports:gdsfileloadVariantExperimentmakeVariantExperimentFromGDSmakeVariantExperimentFromSEQGDSmakeVariantExperimentFromSNPGDSmakeVariantExperimentFromVCFsaveVariantExperimentshowAvailableVariantExperiment
Dependencies:abindaskpassBiobaseBiocGenericsBiostringscrayoncurlDelayedArrayDelayedDataFrameGDSArraygdsfmtgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSeqArraySNPRelateSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| VariantExperiment: A package to represent VCF / GDS files using standard SummarizedExperiment metaphor with on-disk representation. | VariantExperiment-package |
| loadVariantExperiment to load the GDS back-end SummarizedExperiment object into R console. | loadVariantExperiment |
| makeVariantExperimentFromGDS | makeVariantExperimentFromGDS makeVariantExperimentFromSEQGDS makeVariantExperimentFromSNPGDS |
| The function to convert VCF files directly into VariantExperiment object. | makeVariantExperimentFromVCF |
| saveVariantExperiment Save all the assays in GDS format, including in-memory assays. Delayed assays with delayed operations on them are realized while they are written to disk. | saveVariantExperiment |
| ShowAvailable | showAvailable |
| VariantExperiment-class | gdsfile,VariantExperiment-method VariantExperiment VariantExperiment-class |
