UPDhmm
Bioc currentDetecting Uniparental Disomy through NGS trio data
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
Uniparental disomy (UPD) is a genetic condition where an individual inherits both copies of a chromosome or part of it from one parent, rather than one copy from each parent. This package contains a HMM for detecting UPDs through HTS (High Throughput Sequencing) data from trio assays. By analyzing the genotypes in the trio, the model infers a hidden state (normal, father isodisomy, mother isodisomy, father heterodisomy and mother heterodisomy).
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
10 5 exported
Complexity
7.3 avg / 14 max
Call network
10 nodes / 4 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
3,383
Files
50
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
4
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.71
testthat edition
–
CI present
No
CI type
[]
PR gated
No
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
4.1.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Marta Sevilla author maintainer
- Carlos Ruiz-Arenas author