scoreInvHap
Bioc currentGet inversion status in predefined regions
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
scoreInvHap can get the samples' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
11 4 exported
Complexity
3.5 avg / 12 max
Call network
11 nodes / 9 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
2,426
Files
48
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
7
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 16includes a package overview page
- Examples that run
- 100%3 run in a plain check
- Exported functions with examples
- 75%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Refs | list | 22 elements | No other package |
| SNPsR2 | list | 22 elements | No other package |
| hetRefs | list | 22 elements | No other package |
| info | data.frame | 19,416 × 6 | No other package |
| inversionGR | – | – | – |
Topics
People
- Juan R. Gonzalez author maintainer
- Dolors Pelegrí author
- Carlos Ruiz author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scoreInvHap")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 v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.