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.
If you use PhageCocktail, please cite it as:
"PhageCocktail: An R Package to Design Phage Cocktails from Experimental
Phage-Bacteria Infection Networks". Mara Victoria Daz-Galin, Miguel A.
Vega-Rodrguez, Felipe Molina. Computer Methods and Programs in Biomedicine,
221, 106865, Elsevier Ireland, Clare, Ireland, 2022, pp. 1-9, ISSN: 0169-2607.
.