combinePPI: Combine PPI information from databases

In cisPath: Visualization and management of the protein-protein interaction networks.

Description

This method is used to combine the PPI information generated from different databases.

Usage

combinePPI(input, output, mappingFile="", dbNames="", maxEdgeValue=-1)
## S4 method for signature 'character,character'
combinePPI(input, output, mappingFile="", dbNames="", maxEdgeValue=-1)

Arguments

input	Files that contain PPI information (character vector).
output	Output file (character(1)).
mappingFile	Identifier mapping file (character(1)). Generate this file with method getMappingFile.
dbNames	dbNames for input files (character vector).
maxEdgeValue	Filter out PPI information with edge cost greater than this value. (double(1)). Default: no filter.

Details

The input files should follow the format as the output files of the method formatSTRINGPPI, formatPINAPPI, formatSIFfile, or formatiRefIndex. See the files STRINGPPI.txt or PINAPPI.txt as examples. The first four fields contain the Swiss-Prot accession numbers and gene names for two interacting proteins. The PubMedID field should be stated to be NA if unavailable. The evidence field may present an introduction to the evidence. The edgeValue field should be given a value no less than 1. This value will be treated as the cost while identifying the shortest paths. If there is no method available to estimate this value, please give the value as 1.

In some cases, a protein may have several swiss-Prot accession numbers. The parameter mappingFile is used to unify the swiss-Prot accession numbers for proteins from different databases. The proteins whose swiss-Prot accession numbers are not included in the mappingfile will be ignored as well as the intereractions associated to them.

See Also

formatSTRINGPPI, formatPINAPPI, formatSIFfile, formatiRefIndex, cisPath, getMappingFile.

Examples

    library(cisPath)
    inputFile1 <- system.file("extdata", "PINA2PPI.txt", package="cisPath")
    inputFile2 <- system.file("extdata", "iRefIndex.txt", package="cisPath")
    inputFile3 <- system.file("extdata", "STRINGPPI.txt", package="cisPath")
    output <- file.path(tempdir(), "allPPI.txt")
    combinePPI(c(inputFile1, inputFile2, inputFile3), output, maxEdgeValue=1.4)

Example output

Output: /work/tmp/tmp/RtmpavoT1j/allPPI.txt
Maximum edge value: 1.400
Processing file /usr/local/lib/R/site-library/cisPath/extdata/PINA2PPI.txt

Processed 38 lines
Processing file /usr/local/lib/R/site-library/cisPath/extdata/iRefIndex.txt

Processed 100 lines
Processed 125 lines
Processing file /usr/local/lib/R/site-library/cisPath/extdata/STRINGPPI.txt

Processed 163 lines
[1] "/work/tmp/tmp/RtmpavoT1j/allPPI.txt"

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