R: Example Complete Report after the following steps. Blast data...

report {Plasmidprofiler} | R Documentation

## Example Complete Report after the following steps. Blast data from attached blastdata table SRST2 data from attached srst2data table

### Description

read_blast Import the blast file, add column names blast_parser Parse imported file amr_positives Detect AMR positive plasmids read_srst2 Import SRST2 file combine_results Combine SRST2 and Blast zetner_score Add Sureness value amr_presence Add detected AMR to report order_report Arrange report

### Usage

    data(report)

### Format

Dataframe.

### Source

Strains graciously provided by the authors of the following papers: Complete Genome and Plasmid Sequences of Three Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human and Food Sources. 2016 Labbe et al. PMID: 26769926

Complete Sequence of Four Multidrug-Resistant MOBQ1 Plasmids Harboring blaGES-5 Isolated from Escherichia coli and Serratia marcescens Persisting in a Hospital in Canada. 2015 Boyd et al. PMID: 25545311

Colistin-Nonsusceptible Pseudomonas aeruginosa Sequence Type 654 with blaNDM-1 Arrives in North America. 2016 Mataseje et al. PMID: 26824951

### References

None Yet (PubMed)

### Examples

    data(report)

[Package Plasmidprofiler version 0.1.6 Index]