DESCRIPTION

Package: mcCNV
Type: Package
Title: Call copy number variants from whole exome/whole genome sequencing data
Version: 0.1.0
Authors@R: 
    c(person("Dayne L", "Filer", 
             role = c("aut", "cre"), 
             email = "dayne.filer@gmail.com"),
      person("Kirk C", "Wilhelmsen",
             role = c("ctb", "ths")))
Maintainer: Dayne Filer <dayne.filer@gmail.com>
Description: The package provides a framework for performing depth-based copy
    number variation estimation. The package is intended to be used with whole-
    exome sequencing data generated with multiplexed capture (all exomes 
    captured in a single pooled step). The package provides functionality for
    counting depth over provided intervals, then computes the maximum 
    likelihood copy number based on the negative binomial distribution (adapted
    from the 'sSeq' algorithm, <doi:10.1093/bioinformatics/btt143>). Additional
    functionality is provided to simulate read-depth data, helpful for defining
    sequencing depth requirements and selecting prior values.
Encoding: UTF-8
LazyData: true
Imports: 
    Rsamtools,
    matrixStats,
    GenomicRanges,
    GenomeInfoDb,
    IRanges,
    Rfast,
    parallel,
    stats,
    utils
Depends: 
    data.table (>= 1.12.8),
    R (>= 3.6)
RoxygenNote: 7.1.0
Roxygen: list(markdown = TRUE)