Package: RCNA 1.0
Matt Bradley
RCNA: Robust Copy Number Alteration Detection (RCNA)
Detects copy number alteration events in targeted exon sequencing data for tumor samples without matched normal controls. The advantage of this method is that it can be applied to smaller sequencing panels including evaluations of exon, transcript, gene, or even user specified genetic regions of interest. Functions in the package include steps for GC-content correction, calculation of quantile based normal karyotype ranges, and calculation of feature score. Cutoffs for "normal" quantile and score are user-adjustable.
Authors:
RCNA_1.0.tar.gz
RCNA_1.0.tar.gz(r-4.5-noble)RCNA_1.0.tar.gz(r-4.4-noble)
RCNA_1.0.tgz(r-4.4-emscripten)RCNA_1.0.tgz(r-4.3-emscripten)
RCNA.pdf |RCNA.html✨
RCNA/json (API)
NEWS
| # Install 'RCNA' in R: |
| install.packages('RCNA', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- example_obj - Example RCNA_object
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:98c2e3c997. Checks:2 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 03 2025 |
| R-4.5-linux | OK | Jan 03 2025 |
Exports:correct_gc_biascreate_RCNA_objectestimate_feature_scoreestimate_nkrRCNA_analysisRCNA_objectrun_RCNA
Dependencies:clueclustercodetoolsdata.tabledoParallelfBasicsforeachgssiteratorsMASSmodeestR.methodsS3R.ooR.utilsrmutilrpartspatialstablestablediststatiptimeDatetimeSeries
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| correct_gc_bias: Estimate and correct GC bias in coverage | correct_gc_bias correct_gc_bias.default correct_gc_bias.RCNA_object |
| RCNA_object constructor | create_RCNA_object |
| estimate_feature_score: Estimate CNV score for each gene in the annotation file | estimate_feature_score estimate_feature_score.default estimate_feature_score.RCNA_object |
| estimate_nkr: Estimate CNA "normal" karyotype ranges | estimate_nkr estimate_nkr.default estimate_nkr.RCNA_object |
| Example RCNA_object | example_obj |
| RCNA_analysis constructor | RCNA_analysis RCNA_analysis-class |
| RCNA.object definition | RCNA_object RCNA_object-class |
| run_RCNA: Perform RCNA copy number detection workflow | run_RCNA run_RCNA.default run_RCNA.RCNA_object |