formatiRefIndex: Format PPI files downloaded from the iRefIndex database

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 iRefIndex database.

Usage

formatiRefIndex(input, output, taxonId="")
## S4 method for signature '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

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.

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

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)
    
## Not run: 
    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)
    
## End(Not run)

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