cisPath (version 1.12.0)

formatiRefIndex: Format PPI files downloaded from the iRefIndex database

Description

This method is used to format the PPI file which is downloaded from the iRefIndex database.

Usage

formatiRefIndex(input, output, taxonId="")
## S3 method for class 'character,character':
formatiRefIndex(input, output, taxonId="")

Arguments

input

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

output

Output file (character(1)).

taxonId

NCBI taxonomy specie identifier (character(1)). Process only data for this specie. Examples: 9606: Homo sapiens 4932: Saccharomyces cerevisiae 6239: Caenorhabditis elegans 7227: Drosophila melanogaster 10090: Mus musculus 10116: Rattus norvegicus

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 is downloaded from the iRefIndex database (http://irefindex.org/wiki/). Access http://irefindex.org/download/irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6/ to download PPI files with the MITAB2.6 format for different species. If you make use of this file, please cite the iRefIndex database.

References

Razick S. and et al. (2008) iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics, 9, 405 Aranda, B. and et al. (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions, Nat Methods, 8, 528-529.

See Also

cisPath, formatPINAPPI, formatSIFfile, formatSTRINGPPI, combinePPI.

Examples

library(cisPath)
    input <- system.file("extdata", "9606.mitab.100.txt", package="cisPath")
    output <- file.path(tempdir(), "iRefIndex.txt")
    formatiRefIndex(input, output)
    
outputDir <- file.path(getwd(), "cisPath_test")
    dir.create(outputDir, showWarnings=FALSE, recursive=TRUE)
    
    # Download iRefIndex PPI for humans only (compressed:~105M, decompressed:~757M)
    destfile <- file.path(outputDir, "9606.mitab.08122013.txt.zip")
    cat("Downloading...\n")
    httpURL <- "http://irefindex.org/download"
    filePath <- "irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6"
    fileName <- "9606.mitab.08122013.txt.zip"
    URL <- paste(httpURL, filePath, fileName, sep="/")
    download.file(URL, destfile)
    unzip(destfile, overwrite=TRUE, exdir=outputDir)

    # Format iRefIndex PPI
    fileFromiRef <- file.path(outputDir, "9606.mitab.08122013.txt")
    iRefIndex <- file.path(outputDir, "iRefIndex.txt")
    formatiRefIndex(fileFromiRef, output=iRefIndex)