VariantExperiment
Bioc currentA RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
52 8 exported
Complexity
3.5 avg / 15 max
Call network
52 nodes / 82 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
2,867
Files
31
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
44
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
Docs
Roxygen coverage
88.9%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
26.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2019-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
100%
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 7includes a package overview page
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- 83%
- Documented parameters
- 100%
- Return-value docs
- 83%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/bioconductor/variantexperiment on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Example_sampleInfo | data.frame | 90 × 1 | No other package |
Topics
People
- Qian Liu author maintainer
- Martin Morgan author
- Hervé Pagès author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("VariantExperiment")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.