GBScleanR
Bioc currentError correction tool for noisy genotyping by sequencing (GBS) data
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
136 8 exported
Complexity
3.9 avg / 21 max
Call network
136 nodes / 101 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
18,150
Files
114
Compiled share
11.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
71
Internal functions
91
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.14
testthat edition
3
CI present
Yes
CI type
["github-actions"]
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
–
System requirements
2
C++ standard
C++11
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-10-18
Latest release
2026-04-28
Avg cadence
139 days
Cold removal rate
100%
Dep drift
0
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
- 98%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Tomoyuki Furuta author maintainer