prewas: Data Pre-Processing for Bacterial Genome-Wide Association Studies

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).

Version: 1.1.1
Depends: R (≥ 3.5.0)
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)
Published: 2021-04-02
Author: Katie Saund ORCID iD [aut, cre], Zena Lapp ORCID iD [aut], Stephanie Thiede ORCID iD [aut]
Maintainer: Katie Saund <katiephd at umich.edu>
BugReports: https://github.com/Snitkin-Lab-Umich/prewas/issues
License: MIT + file LICENSE
URL: https://github.com/Snitkin-Lab-Umich/prewas
NeedsCompilation: no
Citation: prewas citation info
Materials: README NEWS
CRAN checks: prewas results

Documentation:

Reference manual: prewas.pdf
Vignettes: a primer on prewas

Downloads:

Package source: prewas_1.1.1.tar.gz
Windows binaries: r-devel: prewas_1.1.1.zip, r-release: prewas_1.1.1.zip, r-oldrel: prewas_1.1.1.zip
macOS binaries: r-release (arm64): prewas_1.1.1.tgz, r-release (x86_64): prewas_1.1.1.tgz, r-oldrel: prewas_1.1.1.tgz
Old sources: prewas archive

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