An example of GFF3 formatted genome information.

datasets

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).

Katie Saund

prewas

Data Pre-Processing for Bacterial Genome-Wide Association
Studies

Zena Lapp

Stephanie Thiede

gff function

A character matrix with 110 rows and 9 columns:<dl class="dl-horizontal">
 <dt>Column 1</dt><dd>Chromosome</dd>
 <dt>Column 2</dt><dd>Data source</dd>
 <dt>Column 3</dt><dd>Feature type</dd>
 <dt>Column 4</dt><dd>Feature start position</dd>
 <dt>Column 5</dt><dd>Feature stop position</dd>
 <dt>Column 6</dt><dd>Score</dd>
 <dt>Column 7</dt><dd>Strand</dd>
 <dt>Column 8</dt><dd>Phase</dd>
 <dt>Column 9</dt><dd>Locus ID</dd>
 </dl>

Format

GFF3 file for example genomes — gff

A character matrix with 110 rows and 9 columns:<dl class='dl-horizontal'>
 <dt>Column 1</dt><dd>Chromosome</dd>
 <dt>Column 2</dt><dd>Data source</dd>
 <dt>Column 3</dt><dd>Feature type</dd>
 <dt>Column 4</dt><dd>Feature start position</dd>
 <dt>Column 5</dt><dd>Feature stop position</dd>
 <dt>Column 6</dt><dd>Score</dd>
 <dt>Column 7</dt><dd>Strand</dd>
 <dt>Column 8</dt><dd>Phase</dd>
 <dt>Column 9</dt><dd>Locus ID</dd>
 </dl>

gff: GFF3 file for example genomes

Description

Usage

Arguments

Format