formatSTRINGPPI {cisPath} | R Documentation

## Format PPI file downloaded from the STRING database

### Description

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

### Usage

    formatSTRINGPPI(input, mappingFile, taxonId, output, minScore=700)
    ## S4 method for signature 'character,character,character,character'
    formatSTRINGPPI(input, mappingFile, taxonId, output, minScore=700)

### Arguments

`input` | File downloaded from the STRING database (character(1)).
`mappingFile` | Identifier mapping file (character(1)). Generate this file with method `getMappingFile`.
`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`
`output` | Output file (character(1)).
`minScore` | Filter out PPI information with STRING scores less than this value. (integer(1)). Recommended default 700 (Only consider high confidence interactions).

### Details

The input file is downloaded from the STRING database (http://string-db.org/). The URL of this file is http://string-db.org/newstring_download/protein.links.v9.1.txt.gz. Access http://string-db.org/newstring_download/species.v9.1.txt to determine the parameter `taxonId`. Access http://string-db.org/newstring_cgi/show_download_page.pl for more details.
If you make use of this file, please cite the STRING database.

### Value

Each line of the output file contains Swiss-Prot accession numbers and gene names for two interacting proteins. An edge value is estimated for each link between two interacting proteins. This value is defined as `max(1,log(1000-STRING_SCORE,100))`. This may be treated as the “cost” while determining the shortest paths between proteins. Advanced users can edit the file and change this value for each edge.

### References

Szklarczyk,D. and et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res, 39, D561-D568.

Franceschini,A. and et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res, 41, D808-D815.

UniProt Consortium and others. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40, D71-D75.

### See Also

`cisPath`, `getMappingFile`, `formatPINAPPI`, `formatSIFfile`, `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(), "STRINGPPI.txt")
        fileFromSTRING <- system.file("extdata", "protein.links.txt", package="cisPath")
        formatSTRINGPPI(fileFromSTRING, mappingFile, "9606", output, 700)

    ## 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 STRING PPI for Homo sapiens (compressed:~27M, decompressed:~213M)
        destfile <- file.path(outputDir, "9606.protein.links.v9.1.txt.gz")
        cat("Downloading...\n")
        download.file("http://string-db.org/newstring_download/protein.links.v9.1/9606.protein.links.v9.1.txt.gz", destfile)
        cat("Uncompressing...\n")
        gunzip(destfile, overwrite=TRUE, remove=FALSE)

        # Format STRING PPI
        fileFromSTRING <- file.path(outputDir, "9606.protein.links.v9.1.txt")
        STRINGPPI <- file.path(outputDir, "STRINGPPI.txt")
        formatSTRINGPPI(fileFromSTRING, mappingFile, "9606", output=STRINGPPI, 700)

    ## End(Not run)

[Package cisPath version 1.22.0 Index]