showReferences: Information about reference species

Description Usage Arguments Value Author(s) See Also Examples

Description

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.

Usage

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

Arguments

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.

Value

See description for returnValue

Author(s)

Oliver Philipp [email protected]

See Also

addReference, removeReference, showInteraction

Examples

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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")

Bioconductor-mirror/Path2PPI documentation built on May 31, 2017, 9:43 p.m.