showReferences {Path2PPI} | R Documentation |
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.
showReferences(path2ppi, species = NA, returnValue = NA)
path2ppi |
An object from the class |
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 |
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 |
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")