Introduction | Installation | Background | GDSArray | DelayedDataFrame | VariantExperiment class | slot accessors | Coercion methods | From VCF to VariantExperiment | From GDS to VariantExperiment | customization for certain gds types | Subsetting methods | two-dimensional subsetting | $ subsetting | Range-based operations | Save / load VariantExperiment object | save VariantExperiment object | load VariantExperiment object | Session Info
Package: VariantExperiment 1.27.0
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_1.27.0.tar.gz
VariantExperiment_1.27.0.zip(r-4.7)VariantExperiment_1.27.0.zip(r-4.6)VariantExperiment_1.27.0.zip(r-4.5)
VariantExperiment_1.27.0.tgz(r-4.6-any)VariantExperiment_1.27.0.tgz(r-4.5-any)
VariantExperiment_1.27.0.tar.gz(r-4.7-any)VariantExperiment_1.27.0.tar.gz(r-4.6-any)
VariantExperiment_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VariantExperiment/json (API)
| # 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-1.27.0(bioc 3.24)VariantExperiment-1.26.0(bioc 3.23)
infrastructuredatarepresentationsequencingannotationgenomeannotationgenotypingarray
Last updated from:b4d16125f1. Checks:1 WARNING, 2 NOTE, 2 OK, 5 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 189 | ||
| linux-devel-x86_64 | NOTE | 283 | ||
| source / vignettes | OK | 216 | ||
| linux-release-x86_64 | NOTE | 322 | ||
| macos-release-arm64 | ERROR | 240 | ||
| macos-oldrel-arm64 | ERROR | 138 | ||
| windows-devel | ERROR | 222 | ||
| windows-release | ERROR | 195 | ||
| windows-oldrel | ERROR | 221 | ||
| wasm-release | OK | 124 |
Exports:gdsfileloadVariantExperimentmakeVariantExperimentFromGDSmakeVariantExperimentFromSEQGDSmakeVariantExperimentFromSNPGDSmakeVariantExperimentFromVCFsaveVariantExperimentshowAvailableVariantExperiment
Dependencies:abindBiobaseBiocGenericsBiostringscrayonDelayedArrayDelayedDataFramedigestGDSArraygdsfmtgenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsRhpcBLASctlS4ArraysS4VectorsSeqArraySeqinfoSNPRelateSparseArraySummarizedExperimentXVector
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 |
