VariantFiltering
Bioc currentFiltering of coding and non-coding genetic variants
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
80 9 exported
Complexity
6.3 avg / 43 max
Call network
80 nodes / 62 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
9,550
Files
75
Compiled share
12.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
10
Internal functions
53
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
15
Dep constraint coverage
51.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-06-16
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
18
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 15 (2 internal)includes a package overview page
- Examples that run
- 42%5 run in a plain check · 7 never run
- Exported functions with examples
- 100%
- Documented parameters
- 59%
- Return-value docs
- 67%
- Help pages citing references
- 67%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/rcastelo/variantfiltering on 2026-10-18.
The R CMD check workflow runs on Linux
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| AA_chemical_properties_HanadaGojoboriLi2006 | – | – | – |
| entrezToPhylostrataEnsGene | vector | 19,323 elements | No other package |
| humanCodonUsage | data.frame | 63 × 1 | No other package |
| humanEnsGenePhylostrata | data.frame | 22,154 × 4 | No other package |
| sequence_variant.gSOXPapril2016 | – | – | – |
| uind | – | – | – |
Topics
People
- Robert Castelo author maintainer
- Joan Fernandez contributor
- Dei Martinez Elurbe contributor
- Pau Puigdevall contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("VariantFiltering")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.