results: Results from running prewas() on the example data.
In prewas: Data Pre-Processing for Bacterial Genome-Wide Association Studies

Output from prewas(). results <- prewas::prewas(dna = prewas::vcf, tree = prewas::tree, outgroup = prewas::outgroup, gff = prewas::gff, anc = FALSE)

results

List of 5 objects.

allele_mat: Matrix. Character matrix of nucleotides (alleles). Multiallelic sites represented on multiple lines in the matrix. Dim: 360 x 13. Rows are genomic loci. Columns are samples. Row names include only genomic position and do not have gene information.
bin_mat: Matrix. Binary matrix (nucleotides stored as 0 or 1). Multiallelic sites represented on multiple lines in the matrix. Alleles in overlapping genes are represented on multiple lines in the matrix. Rownames include genomic position and gene. Dim: 1016 x 13. Rows are genomic loci. Columns are samples.
ar_results: Data.frame. Dim: 360 x 1. Rows are genomic loci. The column is the major allele at that position. If anc=TRUE, then this object would be a 306 x 2 data.frame where the first column is the ancestral allele at that position inferred from ancestral reconstruction and the second column is the maximum likelihood probability.
dup: Integer vector. Length = 360. The number refers to the original genomic loci in the VCF file. The occurrence count of the number is one less than the number of alleles. Ex: the 1st genomic locus (Position "1") occurs once in 'dup' indicating that this is a biallelic site. In contrast, the 5th genomic locus in the vcf (Position 18) occurs twice indicating that this is a triallelic site (represented in two rows: 18 and 18.1)
gene_mat: Matrix. Gene-based matrix. Genes with any SNP stored as 1, genes without SNPs stored as 0. Rows are genes. Columns are samples. Dim: 96 x 13.