Data Pre-Processing for Bacterial Genome-Wide Association Studies

Documentation for package ‘prewas’ version 1.1.1

collapse_snps_into_genes	Collapse SNPs into the gene(s) which they are from
collapse_snps_into_genes_by_impact	Collapse SNPs into the gene(s) which they are from and by snpeff impcat
gff	GFF3 file for example genomes
outgroup	Name of outgroup in the phylogenetic tree.
prewas	Preprocess SNPs before bGWAS
results	Results from running prewas() on the example data.
snpeff_vcf	Nucleotide variants in example genome samples with snpeff annotations.
tree	Phylogenetic tree of example genomes
vcf	Nucleotide variants in example genome samples