amr_presence

Dataframe of results produced
by <code><a rd-options="" href="/link/subsampler?package=Plasmidprofiler&version=0.1.6" data-mini-rdoc="Plasmidprofiler::subsampler">subsampler</a></code> or <code><a rd-options="" href="/link/combine_results?package=Plasmidprofiler&version=0.1.6" data-mini-rdoc="Plasmidprofiler::combine_results">combine_results</a></code>

report

Two column DF of plasmid names and genes present produced
by <code><a rd-options="" href="/link/amr_positives?package=Plasmidprofiler&version=0.1.6" data-mini-rdoc="Plasmidprofiler::amr_positives">amr_positives</a></code>

pos.samples


Appends the results of amr_positives to the report
in column AMR_gene, missing have "-" instead


Contains functions developed to combine the results of querying a plasmid database using
short-read sequence typing with the results of a blast analysis against the query results.

Adrian Zetner

Plasmidprofiler

Visualization of Plasmid Profile Results

amr_presence function

Dataframe of results produced
by <code><a rd-options='' href='subsampler'>subsampler</a></code> or <code><a rd-options='' href='combine_results'>combine_results</a></code>

Two column DF of plasmid names and genes present produced
by <code><a rd-options='' href='amr_positives'>amr_positives</a></code>

amr_presence: Adds the AMR_gene column to report

Description

Usage

Arguments

Value

See Also

Examples