combinePPI {cisPath} | R Documentation

## Combine PPI information from databases

### 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)

[Package cisPath version 1.24.0 Index]