YAPSA
Bioc currentYet Another Package for Signature Analysis
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
128 102 exported
Complexity
6.5 avg / 303 max
Call network
128 nodes / 123 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
19,628
Files
153
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
102
Internal functions
22
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
33.3%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
15
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 102includes a package overview page
- Examples that run
- 100%93 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 94%
- Return-value docs
- 100%
- Help pages citing references
- 8%
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 |
|---|---|---|---|
| AlexCosmicArtif_sigInd_df | data.frame | 36 × 8 | No other package |
| AlexCosmicArtif_sig_df | data.frame | 96 × 35 | No other package |
| AlexCosmicValid_sigInd_df | data.frame | 31 × 8 | No other package |
| AlexCosmicValid_sig_df | data.frame | 96 × 40 | No other package |
| AlexInitialArtif_sigInd_df | data.frame | 28 × 8 | No other package |
| AlexInitialArtif_sig_df | data.frame | 96 × 27 | No other package |
| AlexInitialValid_sigInd_df | data.frame | 23 × 8 | No other package |
| AlexInitialValid_sig_df | data.frame | 96 × 22 | No other package |
| COSMIC_subgroups_df | data.frame | 23 × 8 | No other package |
| GenomeOfNl_raw | data.frame | 591 × 8 | No other package |
| MutCat_indel_df | data.frame | 83 × 15 | No other package |
| chosen_signatures_indices_df | data.frame | 7 × 4 | No other package |
| cutoffCosmicArtif_abs_df | data.frame | 10 × 35 | No other package |
| cutoffCosmicArtif_rel_df | data.frame | 10 × 35 | No other package |
| cutoffCosmicValid_abs_df | data.frame | 10 × 30 | No other package |
| cutoffCosmicValid_rel_df | data.frame | 10 × 30 | No other package |
| cutoffInitialArtif_abs_df | data.frame | 10 × 27 | No other package |
| cutoffInitialArtif_rel_df | data.frame | 10 × 27 | No other package |
| cutoffInitialValid_abs_df | data.frame | 10 × 22 | No other package |
| cutoffInitialValid_rel_df | data.frame | 10 × 22 | No other package |
| cutoffPCAWG_ID_WGS_Pid_df | data.frame | 10 × 16 | No other package |
| cutoffPCAWG_SBS_WGSWES_artifPid_df | data.frame | 16 × 65 | No other package |
| cutoffPCAWG_SBS_WGSWES_realPid_df | data.frame | 15 × 47 | No other package |
| exchange_colour_vector | vector | 6 elements | No other package |
| exome_mutCatRaw_df | data.frame | 96 × 70 | No other package |
| lymphomaNature2013_mutCat_df | – | – | – |
| lymphoma_Nature2013_COSMIC_cutoff_exposures_df | data.frame | 7 × 23 | No other package |
| lymphoma_Nature2013_raw_df | data.frame | 128,639 × 8 | No other package |
| lymphoma_PID_df | data.frame | 23 × 1 | No other package |
| lymphoma_test_df | data.frame | 10,113 × 10 | No other package |
| rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df | data.frame | 7 × 23 | No other package |
| sigs_pcawg | – | – | – |
| targetCapture_cor_factors | list | 11 elements | No other package |
Topics
People
- Daniel Huebschmann author maintainer
- Carolin Andresen author
- Zuguang Gu author
- Lea Jopp-Saile author
- Matthias Schlesner author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("YAPSA")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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.