showReferences: Information about reference species
In Path2PPI: Prediction of pathway-related protein-protein interaction networks

Description Usage Arguments Value Author(s) See Also Examples

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.

1	showReferences(path2ppi, species = NA, returnValue = NA)

`path2ppi`	An object from the class `Path2PPI`.
`species`	Either a number between 1 and the number of stored reference species or a character string with the taxonomy id. If no value for `species` is given then information about each stored reference species is provided.
`returnValue`	Character value indicating whether to return a value. "proteins": a data frame containing the proteins associated with the pathway of interest in the corresponding reference species. "interactions": a data frame containing all processed, relevant and non-redundant interactions. "irefindex": a data frame containing all relevant interactions in the raw irefindex format. Is only reasonable if `species` is defined. If no value for `returnValue` is given then only general information is provided.

See description for returnValue

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

addReference, removeReference, showInteraction

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) 

#Get general information about each stored reference species
showReferences(ppi)

#Get general information about reference species with the taxonomy id "9606"
showReferences(ppi, species="9606")

#Get all proteins associated with the pathway of interest 
#and previously given by the user
proteins <- showReferences(ppi, species="9606", returnValue="proteins")

#Get all processed and non-redundant interactions previously 
#determined to be relevant for the pathway of interest
interactions <- showReferences(ppi, species="9606", returnValue="interactions")

#Get all relevant interactions in the detailed irefindex format
irefindex <- showReferences(ppi, species="9606", returnValue="irefindex")