DESCRIPTION

Package: conta
Title: Detect cross-contamination
Version: 0.9.23
Authors@R: as.person(c(
    "Onur Sakarya <osakarya@grailbio.com> [aut, cre]", 
    "TaeHyung Simon Kim <tkim@grailbio.com> [aut]",
    "Christopher Yakym <cyakym@grailbio.com> [aut]",
    "Robert Calef <rcalef@grailbio.com> [aut]"
  ))
Description: Detect contamination from sequencing data. 
    Input data comes in the format of pileup tsv files. Population minor allele
    frequency (MAF) is added through a merge with provided dbSNP vcf file. 
    The contamination module builds a baseline error profile across non-SNP
    alleles and uses this information to calculate the likelihood of each SNP
    to be contaminated. The contamination level that maximizes the likelihood
    across all SNPs is reported as the candidate contamination level, along with
    a call that is made based on the threshold provided, and other related
    metrics and graphics. Chromosomal regions with loss of heterozygosity (LOH)
    are not used for contamination analysis.
Imports:
    data.table,
    dplyr,
    ggplot2,
    hexbin,
    parallel,
    Rcpp,
    reshape2,
    pROC
Depends: R (>= 3.3.1)
License: Apache License (== 2.0) | file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: knitr,
    rmarkdown,
    testthat
VignetteBuilder: knitr
LinkingTo: Rcpp
SystemRequirements: C++11
RoxygenNote: 6.1.1