getMappingFile {cisPath} | R Documentation

## Generate the identifier mapping file

### Description

This method is used to generate the identifier mapping file which is necessary for methods `formatSIFfile` and `formatSTRINGPPI`.

### Usage

    getMappingFile(sprotFile, output, tremblFile="", taxonId="")
    ## S4 method for signature 'character,character'
    getMappingFile(sprotFile, output, tremblFile="", taxonId="")

### Arguments

`sprotFile` | Input: File downloaded from the UniProt database (UniProtKB/Swiss-Prot) (character(1)).
`output` | Output file (character(1)).
`tremblFile` | Input: File downloaded from the UniProt database (UniProtKB/TrEMBL) (character(1)).
`taxonId` | NCBI taxonomy specie identifier (character(1)). This method will process only data for this specie. Default: process all data (recommended).

### Details

UniProtKB/Swiss-Prot: fully annotated curated entries.
UniProtKB/TrEMBL: computer-generated entries enriched with automated classification and annotation.
`sprotFile` is mandatory, while `tremblFile` is optional. If users only want to process the reviewed proteins from the UniProt database, `tremblFile` should be ignored.

All species: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.dat.gz
Taxonomic divisions: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/

uniprot_sprot_archaea.dat.gz and uniprot_trembl_archaea.dat.gz contain all archaea entries.
uniprot_sprot_bacteria.dat.gz and uniprot_trembl_bacteria.dat.gz contain all bacteria entries.
uniprot_sprot_fungi.dat.gz and uniprot_trembl_fungi.dat.gz contain all fungi entries.
uniprot_sprot_human.dat.gz and uniprot_trembl_human.dat.gz contain all human entries.
uniprot_sprot_invertebrates.dat.gz and uniprot_trembl_invertebrates.dat.gz contain all invertebrate entries.
uniprot_sprot_mammals.dat.gz and uniprot_trembl_mammals.dat.gz contain all mammalian entries except human and rodent entries.
uniprot_sprot_plants.dat.gz and uniprot_trembl_plants.dat.gz contain all plant entries.
uniprot_sprot_rodents.dat.gz and uniprot_trembl_rodents.dat.gz contain all rodent entries.
uniprot_sprot_vertebrates.dat.gz and uniprot_trembl_vertebrates.dat.gz contain all vertebrate entries except mammals.
uniprot_sprot_viruses.dat.gz and uniprot_trembl_viruses.dat.gz contain all eukaryotic entries except those from vertebrates, fungi and plants.
We suggest you take a look at the README file before you download these files.

If you make use of these files, please cite the UniProt database.

### Value

The output file contains identifier mapping information which is necessary for methods `formatSIFfile` and `formatSTRINGPPI`. Each line contains both the Ensembl Genomes Protein identifier and the Swiss-Prot accession number for a given protein.

### References

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

### See Also

`cisPath`, `formatSTRINGPPI`, `formatSIFfile`, `combinePPI`.

### Examples

        library(cisPath)
        sprotFile <- system.file("extdata", "uniprot_sprot_human10.dat", package="cisPath")
        output <- file.path(tempdir(), "mappingFile.txt")
        getMappingFile(sprotFile, output, taxonId="9606")

    ## 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)

        # Download protein information file for humans only from UniProt (decompressed:~246M)
        destfile <- file.path(outputDir, "uniprot_sprot_human.dat.gz");
        cat("Downloading...\n")
        download.file("ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_human.dat.gz", destfile)
        gunzip(destfile, overwrite=TRUE, remove=FALSE)

        destfile <- file.path(outputDir, "uniprot_trembl_human.dat.gz");
        cat("Downloading...\n")
        download.file("ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_human.dat.gz", destfile)
        gunzip(destfile, overwrite=TRUE, remove=FALSE)

        # Generate identifier mapping file
        sprotFile <- file.path(outputDir, "uniprot_sprot_human.dat")
        tremblFile <- file.path(outputDir, "uniprot_trembl_human.dat")
        mappingFile <- file.path(outputDir, "mappingFile.txt")
        getMappingFile(sprotFile, output=mappingFile, tremblFile)

    ## End(Not run)

[Package cisPath version 1.34.0 Index]