formatSIFfile: Format PPI file downloaded from the PINA2 database (SIF...

In cisPath: Visualization and management of the protein-protein interaction networks.

Description

This method is used to format the PPI file which is downloaded from the PINA2 database (SIF Format).

Usage

formatSIFfile(input, mappingFile, output)
## S4 method for signature 'character,character,character'
formatSIFfile(input, mappingFile, output)

Arguments

input	File downloaded from the PINA2 database (SIF Format) (character(1)).
mappingFile	Identifier mapping file (character(1)). Generate this file with method getMappingFile.
output	Output file (character(1)).

Details

The input file (SIF Format) is downloaded from PINA2 database (http://cbg.garvan.unsw.edu.au/pina/).
Access http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do to download PPI files with the SIF format for different species.
If you make use of this file, please cite the PINA database.

Value

Each line of the output file contains Swiss-Prot accession numbers and gene names for two interacting proteins. The edge value will be assigned as 1 for each link between two interacting proteins. This may be treated as the “cost” while identifying the shortest paths between proteins. Advanced users can edit the file and change this value for each edge.

References

Cowley, M.J. and et al. (2012) PINA v2.0: mining interactome modules. Nucleic Acids Res, 40, D862-865.

Wu, J. and et al. (2009) Integrated network analysis platform for protein-protein interactions. Nature methods, 6, 75-77.

See Also

cisPath, getMappingFile, formatPINAPPI, formatSTRINGPPI, formatiRefIndex, combinePPI.

Examples

    library(cisPath)
    
    # Generate the identifier mapping file 
    input <- system.file("extdata", "uniprot_sprot_human10.dat", package="cisPath")
    mappingFile <- file.path(tempdir(), "mappingFile.txt")
    getMappingFile(input, output=mappingFile, taxonId="9606")
    
    # Format the file downloaded from STRING database
    output <- file.path(tempdir(), "PINA2PPI.txt")
    fileFromPINA2 <- system.file("extdata", "Homo_sapiens_PINA2.sif", package="cisPath")
    formatSIFfile(fileFromPINA2, mappingFile, output)
    
## Not run: 
    if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")
    BiocManager::install("R.utils")
    library(R.utils)
    
    outputDir <- file.path(getwd(), "cisPath_test")
    dir.create(outputDir, showWarnings=FALSE, recursive=TRUE)
    
    # Generate the identifier mapping file 
    fileFromUniProt <- file.path(outputDir, "uniprot_sprot_human.dat")
    mappingFile <- file.path(outputDir, "mappingFile.txt")
    getMappingFile(fileFromUniProt, output=mappingFile)
    
    # Download PINA2 PPI (SIF format) for humans only (~2.8M)
    destfile <- file.path(outputDir, "Homo_sapiens.sif")
    cat("Downloading...\n")
    download.file("http://cbg.garvan.unsw.edu.au/pina/download/Homo%20sapiens-20140521.sif", destfile)
    
    # Format PINA2 PPI
    fileFromPINA2 <- file.path(outputDir, "Homo_sapiens.sif")
    PINA2PPI <- file.path(outputDir, "PINA2PPI.txt")
    formatSIFfile(fileFromPINA2, mappingFile, output=PINA2PPI)
    
## End(Not run)    

cisPath documentation built on Nov. 8, 2020, 7:15 p.m.