showReferences {Path2PPI} | R Documentation

## Information about reference species

### 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

    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 MolBI-software@bioinformatik.uni-frankfurt.de

### See Also

`addReference`, `removeReference`, `showInteraction`

### 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)

    #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")

[Package Path2PPI version 1.14.0 Index]