trio
Bioc currentTesting of SNPs and SNP Interactions in Case-Parent Trio Studies
Release Lineage
Entered 2.13 · Oct 15, 2013
Current · Requires R 4.6
Description
Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
441 58 exported
Complexity
6.5 avg / 43 max
Call network
441 nodes / 477 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
31,417
Files
95
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
58
Internal functions
187
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
13.3%
Unsafe pattern score
12
Dep constraint coverage
11.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.0.1
System requirements
–
C++ standard
–
License
LGPL-2
License flags
SPDX valid, OSI approved
History
Versions
26
First release
2013-10-14
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 37
- Examples that run
- 94%34 run in a plain check · 2 never run
- Exported functions with examples
- 97%
- Documented parameters
- 99%
- Return-value docs
- 97%
- Help pages citing references
- 73%
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 |
|---|---|---|---|
| LDdata | matrix | 500 × 50 | 2 packages |
| freq.hap | data.frame | 20 × 3 | 2 packages |
| mat.test | matrix | 300 × 6 | 2 packages |
| prob.mat.test | matrix | 334 × 180 | 2 packages |
| simuBkMap | data.frame | 66 × 3 | 2 packages |
| step3way | list | 4 elements | 2 packages |
| trio.gen.err | data.frame | 60 × 7 | 2 packages |
| trio.gen1 | data.frame | 300 × 12 | 2 packages |
| trio.gen2 | data.frame | 300 × 12 | 2 packages |
| trio.ped.err | data.frame | 300 × 26 | 2 packages |
| trio.ped1 | data.frame | 300 × 26 | 2 packages |
| trio.ped2 | data.frame | 300 × 26 | 2 packages |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("trio")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.