PureCN
Bioc currentCopy number calling and SNV classification using targeted short read sequencing
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
253 44 exported
Complexity
5 avg / 141 max
Call network
253 nodes / 416 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
17,685
Files
200
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
44
Internal functions
207
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
10.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-07-01
Latest release
2026-04-28
Avg cadence
186 days
Cold removal rate
100%
Dep drift
20
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 49
- Examples that run
- 98%44 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 95%
- Help pages citing references
- 16%
Repository practices
5 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/lima1/purecn on 2026-10-25.
The R CMD check workflow runs on Linux and macOS, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| centromeres | list | 3 elements | 2 packages |
| ex1_gcgene | data.frame | 3 × 2 | No other package |
| ex1_intervals | data.frame | 3 × 1 | No other package |
| ex1_intervals_headered | – | – | – |
| ex2_intervals | data.frame | 5 × 1 | No other package |
| example_allelic_counts | – | – | – |
| example_allelic_counts_empty | – | – | – |
| example_gatk4_denoised_cr | – | – | – |
| example_intervals | data.frame | 10,049 × 6 | No other package |
| example_intervals_tiny | data.frame | 496 × 6 | No other package |
| example_intervals_tiny_ot | – | – | – |
| example_logratio | data.frame | 21 × 2 | No other package |
| example_normal | data.frame | 10,049 × 4 | No other package |
| example_normal2 | data.frame | 10,049 × 4 | No other package |
| example_normal_tiny | data.frame | 496 × 5 | No other package |
| example_seg | data.frame | 54 × 6 | No other package |
| example_tumor | data.frame | 10,049 × 4 | No other package |
| example_tumor2 | data.frame | 10,049 × 5 | No other package |
| example_tumor_tiny | data.frame | 496 × 5 | No other package |
| issue184_2_mb | – | – | – |
| purecn.DNAcopy.bdry | vector | 1,326 elements | No other package |
| purecn.example.output | list | 3 elements | No other package |
| test_coverage_overlapping_intervals | data.frame | 5 × 3 | No other package |
Topics
People
- Markus Riester author maintainer
- Angad P. Singh author
Cite
Cite this package
Run in R for the authors' entry:
citation("PureCN")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13029-016-0060-z.
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.