PhageCocktail: Design of the Best Phage Cocktail

There are 4 possible methods: "ExhaustiveSearch"; "ExhaustivePhi"; "ClusteringSearch"; and "ClusteringPhi". "ExhaustiveSearch"–> gives you the best phage cocktail from a phage-bacteria infection network. It checks different phage cocktail sizes from 1 to 7 and only stops before if it lyses all bacteria. Other option is when users have decided not to obtain a phage cocktail size higher than a limit value. "ExhaustivePhi"–> firstly, it finds Phi out. Phi is a formula indicating the necessary phage cocktail size. Phi needs nestedness temperature and fill, which are internally calculated. This function will only look for the best combination (phage cocktail) with a Phi size. "ClusteringSearch"–> firstly, an agglomerative hierarchical clustering using Ward's algorithm is calculated for phages. They will be clustered according to bacteria lysed by them. PhageCocktail() chooses how many clusters are needed in order to select 1 phage per cluster. Using the phages selected during the clustering, it checks different phage cocktail sizes from 1 to 7 and only stops before if it lyses all bacteria. Other option is when users have decided not to obtain a phage cocktail size higher than a limit value. "ClusteringPhi"–> firstly, an agglomerative hierarchical clustering using Ward's algorithm is calculated for phages. They will be clustered according to bacteria lysed by them. PhageCocktail() chooses how many clusters are needed in order to select 1 phage per cluster. Once the function has one phage per cluster, it calculates Phi. If the number of clusters is less than Phi number, it will be changed to obtain, as minimum, this quantity of candidates (phages). Then, it calculates the best combination of Phi phages using those selected during the clustering with Ward algorithm.

Version: 1.0.0
Imports: readxl, stringr, factoextra, bipartite, smerc, RJSONIO
Published: 2021-07-14
Author: Maria Victoria Diaz-Galian ORCID iD [aut, cre], Miguel A. Vega-Rodriguez ORCID iD [aut], Felipe Molina ORCID iD [aut]
Maintainer: Maria Victoria Diaz-Galian <mvdiazgalian at unex.es>
License: GPL-3
NeedsCompilation: no
CRAN checks: PhageCocktail results

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Reference manual: PhageCocktail.pdf
Package source: PhageCocktail_1.0.0.tar.gz
Windows binaries: r-devel: PhageCocktail_1.0.0.zip, r-release: PhageCocktail_1.0.0.zip, r-oldrel: PhageCocktail_1.0.0.zip
macOS binaries: r-release (arm64): PhageCocktail_1.0.0.tgz, r-release (x86_64): PhageCocktail_1.0.0.tgz, r-oldrel: PhageCocktail_1.0.0.tgz

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