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  [aut,
cre],
Zena Lapp [aut],
Stephanie Thiede
[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:
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