decompTumor2Sig
Bioc currentDecomposition of individual tumors into mutational signatures by signature refitting
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
66 24 exported
Complexity
6.5 avg / 51 max
Call network
66 nodes / 121 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
10,536
Files
132
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
24
Internal functions
42
Recent export changes
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
–
Unsafe pattern score
0
Dep constraint coverage
4.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-02
Latest release
2026-07-21
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
- Help pages
- 66 (41 internal)includes a package overview page
- Examples that run
- 100%24 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 100%
- Fix: relpaced non existent default URL for readAlexandrovSignatures(); NOTE: in future versions, no default will be specified anymore!
From inst/NEWS in the release
Repository practices
Checks run against github.com/rmpiro/decomptumor2sig on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| G | – | – | – |
| Nik-Zainal_PMID_22608084-MPF | – | – | – |
| Nik-Zainal_PMID_22608084-pmsignature-sig1 | data.frame | 5 × 6 | No other package |
| Nik-Zainal_PMID_22608084-pmsignature-sig2 | data.frame | 5 × 6 | No other package |
| Nik-Zainal_PMID_22608084-pmsignature-sig3 | data.frame | 5 × 6 | No other package |
| Nik-Zainal_PMID_22608084-pmsignature-sig4 | data.frame | 5 × 6 | No other package |
| Param | – | – | – |
| genomes | list | 21 elements | No other package |
| signatures | list | 15 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- Rosario M. Piro author maintainer
- Sandra Krueger contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("decompTumor2Sig")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.