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.
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
10,535
Files
132
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
24
Internal functions
42
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
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
2026-04-28
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
- Examples that run
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- References docs
- 100%
Topics
Depended on by (1)
Bioconductor (1)
People
- Rosario M. Piro author maintainer
- Sandra Krueger contributor