DESCRIPTION

Package: ZygosityPredictor
Type: Package
Title: Package for prediction of zygosity for variants/genes in NGS data
Version: 1.10.3
Date: 2022-10-26
Authors@R: c(
  person("Marco", "Rheinnecker", 
    email="marco.rheinnecker@dkfz-heidelberg.de", 
    role = c("aut", "cre"),
    comment=c(ORCID="0009-0009-7181-3977")), 
  person("Marc", "Ruebsam", 
    role = c("aut")),
  person("Daniel", "Huebschmann", 
    role = c("aut")),  
  person("Martina", "Froehlich", 
    role = c("aut")),
  person("Barbara", "Hutter", 
    role = c("aut"))
    )
Imports: 
    GenomicAlignments, 
    GenomicRanges, 
    Rsamtools, 
    IRanges, 
    VariantAnnotation, 
    DelayedArray, 
    dplyr, 
    stringr, 
    purrr, 
    tibble,
    methods,
    igraph
License: GPL-2
Description: The ZygosityPredictor allows to predict how many copies of a gene are affected by small variants. In addition to the basic calculations of the affected copy number of a variant, the Zygosity-Predictor can integrate the influence of several variants on a gene and ultimately make a statement if and how many wild-type copies of the gene are left. This information proves to be of particular use in the context of translational medicine. For example, in cancer genomes, the Zygosity-Predictor can address whether unmutated copies of tumor-suppressor genes are present. Beyond this, it is possible to make this statement for all genes of an organism. The Zygosity-Predictor was primarily developed to handle SNVs and INDELs (later addressed as small-variants) of somatic and germline origin. In order not to overlook severe effects outside of the small-variant context, it has been extended with the assessment of large scale deletions, which cause losses of whole genes or parts of them.
RoxygenNote: 7.2.3
Encoding: UTF-8
biocViews: BiomedicalInformatics, FunctionalPrediction, SomaticMutation, GenePrediction
Depends: 
    R (>= 4.3.0)
LazyData: false
Suggests: 
    knitr,
    rmarkdown,
    testthat,
    BiocStyle
VignetteBuilder: knitr