predictPPI {Path2PPI} | R Documentation

## Prediction of the PPI

### Description

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.

### Usage

    predictPPI(path2ppi, mode="both", h.thresh=1e-05,
               h.range=c(1e-100, 1e-20), i.thresh=0.7,
               consider.complexes=FALSE, max.complex.size=5,
               decline.self.interaction.ref=FALSE,
               decline.self.interaction.tar=TRUE,
               verbose=TRUE)

### Arguments

`path2ppi` | An object of the class `Path2PPI`.
`mode` | Which interaction from the reference species should be taken into account. "both": both interactors of an interaction has to be in the initial protein list previously inserted by the user (recommended if it is a large network or many proteins were initially defined, respectively). "one": only one of the interactors of each reference interaction has to be in the initial protein list (may lead to very large networks).
`h.thresh` | E-value cutoff at which each homologous relationship definitely will be declined (see also `h.range` argument).
`h.range` | Numeric vector consisting of two values. The first value indicates the lower border (smallest E-value). Each E-value which is equal or less than this border is scored with 1 (best). The second value indicates the upper border (biggest E-value). Each E-value which is equal or greater than this border is scored with 0 (worst).
`i.thresh` | Numeric. Threshold for accepted interactions. If the computed prediction score for an interaction is less than `i.thresh` it will be declined.
`consider.complexes` | Logical. If `TRUE` then interactions are also considered which actually indicate an association of the current protein to one bigger protein complex. This may lead to very large networks if `mode="one"` since all other proteins of this complex are considered as well, i.e., each protein in such complexes are considered to interact with each other protein of this complex. If `mode="both"` then each protein of an complex has to be in the initial protein list to consider each interaction (see details).
`max.complex.size` | Numeric. Is only considered if `consider.complexes=TRUE`. The maximum size of complexes to be considered.
`decline.self.interaction.ref` | Logical. If `TRUE` then all self interactions from reference species are declined.
`decline.self.interaction.tar` | Logical. If `TRUE` then all predicted self interactions in target species are declined.
`verbose` | Logical. `FALSE` hides messages in the output.

### Details

Difference of `h.thresh` and `h.range`: If only one protein in the target species was found to be homologous to a current reference species protein and this homology was rated with an E-value which is equal or smaller than `h.thresh` it is scored with 1 (even if the E-value is larger than the upper border of `h.range`). See package vignette for more details.

Use the complex arguments with care, since each complex may lead to a vast amount of interactions, i.e., each protein is considered to interact with each other of this complex; e.g. if there are 10 proteins involved in one complex, this would lead to 10 over 2 = 45 interactions.

### Value

An object of the class `Path2PPI` with predicted PPI.

### Author(s)

Oliver Philipp MolBI-software@bioinformatik.uni-frankfurt.de

### See Also

`plot.Path2PPI`, `homologyScore`

### Examples

    data(ai) #Load test data set

    ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")
    ppi <- addReference(ppi, "Homo sapiens", "9606", human.ai.proteins,
                        human.ai.irefindex, pa2human.ai.homologs)
    ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292",
                        yeast.ai.proteins, yeast.ai.irefindex,
                        pa2yeast.ai.homologs)

    #Using the default settings leads to 8 predicted interactions in the
    #target species
    ppi <- predictPPI(ppi)

    #Consider complexes where each complex is allowed to be up to 10 proteins
    #large. For this smaller pathway only one more interaction was predicted when
    #considering larger complexes.
    ppi <- predictPPI(ppi,consider.complexes=TRUE,max.complex.size=10)

    #We can be less strict and decrease h.range what obviously increases the
    #number of predicted interactions to 13
    ppi <- predictPPI(ppi,h.range=c(1e-60,1e-20))

[Package Path2PPI version 1.10.0 Index]