Path2PPI-class {Path2PPI} | R Documentation |
"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.
Path2PPI(...)
... |
Argument list (see Note below). |
An instance of the class Path2PPI
.
pathway
:Object of class "character"
targetSpecies
:Object of class ".TargetSpecies"
referenceContainer
:Object of class
".ReferenceContainer"
h.thresh
:Object of class "numeric"
h.range
:Object of class "numeric"
i.thresh
:Object of class "numeric"
consider.complexes
:Object of class "logical"
max.complex.size
:Object of class "numeric"
raw.ppi
:Object of class "data.frame"
ppi
:Object of class "data.frame"
addReference
signature(path2ppi = "Path2PPI")
getHybridNetwork
signature(path2ppi = "Path2PPI")
getPPI
signature(path2ppi = "Path2PPI")
initialize
signature(.Object = "Path2PPI")
plot.Path2PPI
signature(x = "Path2PPI")
predictPPI
signature(path2ppi = "Path2PPI")
removeReference
signature(path2ppi = "Path2PPI")
show
signature(object = "Path2PPI")
showInteraction
signature(path2ppi = "Path2PPI")
showReferences
signature(path2ppi = "Path2PPI")
Arguments to Path2PPI()
and the new
method are obligatory
and must be named if they differ from this order:
pathway | A character string with the name of the pathway which has to be predicted. |
targetName | A character string giving the taxonomy name of the target species. |
targetId | A character string giving the taxonomy identifier of the target species. |
Oliver Philipp MolBI-software@bioinformatik.uni-frankfurt.de
ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145") ppi