cisPath (version 1.12.0)

formatPINAPPI: Format PPI files downloaded from the PINA database (MITAB Format)

Description

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

Usage

formatPINAPPI(input, output)
## S3 method for class 'character,character':
formatPINAPPI(input, output)

Arguments

input

File downloaded from the PINA database (character(1)).

output

Output file (character(1)).

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.

Details

The input file (MITAB Format) is downloaded from the PINA 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 MITAB format for different species. If you make use of this file, please cite the PINA database.

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, formatSIFfile, formatiRefIndex, formatSTRINGPPI, combinePPI.

Examples

library(cisPath)
    input <- system.file("extdata", "Homo_sapiens_PINA100.txt", package="cisPath")
    output <- file.path(tempdir(), "PINAPPI.txt")
    formatPINAPPI(input, output)
    
outputDir <- file.path(getwd(), "cisPath_test")
    dir.create(outputDir, showWarnings=FALSE, recursive=TRUE)
    
    # Download PINA PPI (MITAB format) for humans only (~96M)
    destfile <- file.path(outputDir, "Homo_sapiens.txt")
    cat("Downloading...\n")
    download.file("http://cbg.garvan.unsw.edu.au/pina/download/Homo%20sapiens-20121210.txt", destfile)

    # Format PINA PPI
    fileFromPINA <- file.path(outputDir, "Homo_sapiens.txt")
    PINAPPI <- file.path(outputDir, "PINAPPI.txt")
    formatPINAPPI(fileFromPINA, output=PINAPPI)