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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.
| Version: | 1.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | doParallel, methods, utils, modeest, data.table, foreach, R.utils |
| Suggests: | knitr, rmarkdown, usethis |
| Published: | 2024-12-03 |
| DOI: | 10.32614/CRAN.package.RCNA |
| Author: | Matt Bradley [aut, cre] |
| Maintainer: | Matt Bradley <mbradley at emmes.com> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Materials: | README NEWS |
| CRAN checks: | RCNA results |
| Reference manual: | RCNA.pdf |
| Vignettes: |
Detecting Copy Number Variation on Targeted Exon Sequencing with RCNA (source) |
| Package source: | RCNA_1.0.tar.gz |
| Windows binaries: | r-devel: RCNA_1.0.zip, r-release: RCNA_1.0.zip, r-oldrel: RCNA_1.0.zip |
| macOS binaries: | r-release (arm64): RCNA_1.0.tgz, r-oldrel (arm64): RCNA_1.0.tgz, r-release (x86_64): RCNA_1.0.tgz, r-oldrel (x86_64): RCNA_1.0.tgz |
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