Package: CNAqc
Type: Package
Title: CNAqc - Copy Number Analysis quality check
Version: 1.1.2
Author: Giulio Caravagna
Maintainer: Giulio Caravagna <gcaravagn@gmail.com>
Authors@R: c(
    person("Giulio", "Caravagna", , "gcaravagn@gmail.com", role = c("aut", "cre"),
      comment = c(ORCID = "0000-0003-4240-3265")
    ),
    person("Riccardo", "Bergamin", , "ric.b.91@gmail.com", role = c("ctb")),
    person("Nicola", "Calonaci", , "nicola.calonaci@gmail.com", role = c("ctb")),
    person("Salvatore", "Milite", , "militesalvatore@gmail.com", role = c("ctb")),
    person("Alice", "Antonello", , "aliceantonello9@gmail.com", role = c("ctb"))    
  )
Description: CNAqc is a package to provide a set of metrics to quality control (QC) 
  allele-specific Copy Number Alteration (CNA) calls, somatic mutations and tumour purity determined 
  from bulk sequencing assays. The package provides statistical measures to quantify the 
  concordance between mutation and CNAs, exploiting the combinatorial relation between allelic 
  imbalance in CNA segments and variant allelic frequencies (VAFs) of somatic mutations. Distinct
  peak matching procedures for VAFs can be used to QC clonal and subclonal copy numbers.
  Quantitative metrics and plots for data exploration are also available, allowing for an intuitive 
  assessment of the goodness of somatic calls. QC metrics computed by CNAqc can also be used to 
  re-parametrize a copy number caller and increase the quality of the somatic calls. The tools is general and can
  be applied downstream of any bioinformatics pipeline. Routines to determine Cancer Cell Franctions (CCFs)
  for each mutation are also available, along with a model of CCF uncertainty that can be used to identify
  high-quality CCF calls for downstream analyses. 
License: GPL (>= 3) + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6)
biocViews:
Imports: Rhtslib, Rsamtools, GenomicRanges, crayon, ggpubr, ggrepel,
        BMix, vcfR, clisymbols, RColorBrewer, VariantAnnotation,
        easypar, gtools, graphics, stats, grDevices, utils, magrittr,
        dplyr, ggplot2, cli, tibble, tidyr, akima, AnnotationDbi,
        cowplot, ggsci, peakPick, progress, readr, R.utils,
        ComplexHeatmap, scales, data.table
Remotes: caravagn/pio, caravagnalab/BMix, caravagn/easypar,
        cran/peakPick
RoxygenNote: 7.3.2
Suggests: knitr, rmarkdown, org.Hs.eg.db, Organism.dplyr, mclust,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/caravagnalab/CNAqc
BugReports: https://github.com/caravagnalab/CNAqc/issues
Config/testthat/edition: 3
Built: R 4.4.3; ; 2025-05-27 12:37:34 UTC; unix
