snpStats
Bioc currentSnpMatrix and XSnpMatrix classes and methods
Release Lineage
Entered 2.8 · Apr 14, 2011
Current · Requires R 4.6
Description
Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
177 47 exported
Complexity
11.4 avg / 124 max
Call network
177 nodes / 207 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
21,639
Files
145
Compiled share
55.5%
Has compiled src
Yes
Language breakdown
API
Exported functions
47
Internal functions
6
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
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
31
First release
2011-05-09
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 55includes a package overview page
- Examples that run
- 78%35 run in a plain check · 10 hold no code
- Exported functions with examples
- 87%
- Documented parameters
- 98%
- Return-value docs
- 95%
- Help pages citing references
- 24%
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 |
|---|---|---|---|
| Asnps | data.frame | 9,445 × 2 | 2 packages |
| Autosomes | SnpMatrix | 400 × 9,445 | 2 packages |
| Xchromosome | XSnpMatrix | 400 × 155 | 2 packages |
| Xsnps | data.frame | 155 × 1 | 2 packages |
| ceph.1mb | SnpMatrix | 90 × 603 | No other package |
| genotypes | SnpMatrix | 3,017 × 43 | No other package |
| pedData | data.frame | 3,017 × 6 | No other package |
| snp.support | data.frame | 28,501 × 4 | 2 packages |
| snps.10 | SnpMatrix | 1,000 × 28,501 | 2 packages |
| subject.data | data.frame | 400 × 4 | 2 packages |
| subject.support | data.frame | 1,000 × 2 | 2 packages |
| support.ld | data.frame | 603 × 5 | No other package |
| yri.1mb | SnpMatrix | 90 × 603 | No other package |
Topics
Depended on by (19)
Show all 33 packagesHide all 33 packages
Bioconductor (14)
CRAN (5)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("snpStats")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.