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).
|Author||Katie Saund [aut, cre] (<https://orcid.org/0000-0002-6214-6713>), Zena Lapp [aut] (<https://orcid.org/0000-0003-4674-2176>), Stephanie Thiede [aut] (<https://orcid.org/0000-0003-0173-4324>)|
|Maintainer||Katie Saund <firstname.lastname@example.org>|
|License||MIT + file LICENSE|
|Package repository||View on CRAN|
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