DESCRIPTION

Package: prewas
Type: Package
Title: Data Pre-Processing for Bacterial Genome-Wide Association Studies
Version: 1.1.1
Authors@R: c(
    person("Katie", "Saund", 
           email = "katiephd@umich.edu", 
           role = c("aut", "cre"), 
           comment = c(ORCID = "0000-0002-6214-6713")),
    person("Zena", "Lapp",
           email = "zenalapp@umich.edu",
           role = "aut", 
           comment = c(ORCID = "0000-0003-4674-2176")), 
    person("Stephanie", "Thiede",
           email = "thiede@umich.edu", 
           role = "aut",
           comment = c(ORCID = "0000-0003-0173-4324")))
Description: Standardize the pre-processing of genomic variants before 
    performing a bacterial genome-wide association study (bGWAS). 'prewas'
    creates a variant matrix (where each row is a variant, each column is a 
    sample, and the entries are presence - 1 - or absence - 0 - of the variant) 
    that can be used as input for bGWAS tools. When creating the binary variant
    matrix, 'prewas' can perform 3 pre-processing steps including: dealing with 
    multiallelic SNPs, (optional) dealing with SNPs in overlapping genes, and 
    choosing a reference allele. 'prewas' can output matrices for use with both 
    SNP-based bGWAS and gene-based bGWAS. This method is described in Saund et 
    al. (2020) <doi:10.1099/mgen.0.000368>. 'prewas' can also provide 
    gene matrices for variants with specific annotations from the 'SnpEff' 
    software (Cingolani et al. 2012).
URL: https://github.com/Snitkin-Lab-Umich/prewas
BugReports: https://github.com/Snitkin-Lab-Umich/prewas/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
RoxygenNote: 7.1.1
Imports: 
    ape (>= 5.3), 
    future (>= 1.15.1),
    future.apply (>= 1.3.0), 
    phangorn (>= 2.5.5), 
    stats (>= 3.5.0),
    vcfR (>= 1.8.0), 
    utils (>= 3.5.0),
    methods (>= 3.5.0)
Suggests: 
    testthat (>= 2.2.1),
    knitr (>= 1.24),
    rmarkdown (>= 1.15)
VignetteBuilder: knitr
Date: 2021-04-01