report: Example Complete Report after the following steps. Blast data...
In phac-nml/plasmidprofiler: Visualization of Plasmid Profile Results
report 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)
phac-nml/plasmidprofiler documentation built on June 11, 2022, 11:25 a.m.
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| report | 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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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