R Graphical Manual

Last data update: 2014.03.03

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Path2PPI-class (Package: Path2PPI) : Class code{"Path2PPI"

An instance of the class Path2PPI is the major object in the Path2PPI package. It manages all reference species and the target species. The prediction algorithm is implemented in this class as well.

● Data Source: BioConductor
● Keywords:
● Alias: Path2PPI, Path2PPI-class, addReference,Path2PPI-method, getHybridNetwork,Path2PPI-method, getPPI,Path2PPI-method, initialize,Path2PPI-method, plot.Path2PPI,Path2PPI-method, predictPPI,Path2PPI-method, removeReference,Path2PPI-method, show,Path2PPI-method, showInteraction,Path2PPI-method, showReferences,Path2PPI-method
● 0 images

addReference (Package: Path2PPI) :

Adds reference species to an object from the class Path2PPI.

● Data Source: BioConductor
● Keywords:
● Alias: addReference
● 0 images

getHybridNetwork (Package: Path2PPI) :

Get the hybrid network of the previously predicted PPI. The hybrid network consists of all relevant interactions from the reference species, the predicted interactions in the target species and all relevant homologous relationships.

● Data Source: BioConductor
● Keywords:
● Alias: getHybridNetwork
● 0 images

getPPI (Package: Path2PPI) :

Get the predicted PPI of an Path2PPI object consisting of each predicted interaction and protein in the target species.

● Data Source: BioConductor
● Keywords:
● Alias: getPPI
● 0 images

homologyScore (Package: Path2PPI) :

Computes the homology scores based on the BLAST E-value. This function is used by the predictPPI method to compute homology scores to decide whether an interaction in a reference species is adopted to the target species (see package vignette for a detailed description). It can be used to test which E-values lead to which scores given a predefined E-value range.

● Data Source: BioConductor
● Keywords:
● Alias: homologyScore
● 0 images

plot.Path2PPI (Package: Path2PPI) :

Plots the predicted PPI in three different ways. Depending on the type argument it manages the specific layout settings and finally uses the plot function of the igraph package.

● Data Source: BioConductor
● Keywords:
● Alias: plot.Path2PPI
● 3 images

predictPPI (Package: Path2PPI) :

Major method of the Path2PPI class to predict the final PPI in the target species using the information available from the stored reference species. Different values for the arguments of this method can lead to different PPI networks, differing in the degree of reliability and strictness.

● Data Source: BioConductor
● Keywords:
● Alias: predictPPI
● 0 images

removeReference (Package: Path2PPI) :

Remove reference species previously attached to an object from the class Path2PPI.

● Data Source: BioConductor
● Keywords:
● Alias: removeReference
● 0 images

showInteraction (Package: Path2PPI) :

Use showInteraction to get detailed information about one interaction of the predicted PPI.

● Data Source: BioConductor
● Keywords:
● Alias: showInteraction, showInteraction-methods
● 0 images

showReferences (Package: Path2PPI) :

Get information about the currently stored reference species. If indicated by returnValue a data frame - containing information about each protein or interaction - is provided as well.

● Data Source: BioConductor
● Keywords:
● Alias: showReferences
● 0 images