collapse_snps_into_genes_by_impact

bin_mat

gene_vec

Character. Vector of predicted functional impacts.

predicted_impact

Character. Vector or single string of impacts of
interest.

snpeff_grouping

Collapse SNPs into the gene(s) which they are from and by snpeff impcat

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).

collapse_snps_into_genes_by_impact: Collapse SNPs into the gene(s) which they are from and by snpeff impcat

Description

Usage

Arguments

Value