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).

Package details

AuthorKatie Saund [aut, cre] (<>), Zena Lapp [aut] (<>), Stephanie Thiede [aut] (<>)
MaintainerKatie Saund <>
LicenseMIT + file LICENSE
Package repositoryView on CRAN
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prewas documentation built on April 2, 2021, 5:06 p.m.