unWantedComp {ScISI} | R Documentation

## A function to manually remove protein complexes from some in silico interactome

### Description

This function takes in an in silico interactome by its bipartite graph representation and a character vector of complex ID's. The function parses through the column names of the in silico interactome and removes those columns whose names are found in the character vector.

### Usage

    unWantedComp(ISI, unwantedComplex = c("GO:0000262", "GO:0000228",
    "GO:0000775", "GO:0010008", "GO:0005792", "GO:0005768", "GO:0005769",
    "GO:0005770", "GO:0005777", "GO:0005844", "GO:0001400"), unwantedGenes =
    c("RNA_TLC1", "SNRNA_NME1","RNA_RNASE-P"))

### Arguments

`ISI` | The in silico interactome as a bipartite graph
`unwantedComplex` | A character vector. Each entry is a protein complex id for which should be removed from the interactome.
`unwantedGenes` | A character vector of gene names that will be deleted from the row indexing set of the in silico interactome.

### Value

An incidence matrix. A new matrix with those columns indexed by unwantedComplex removed. It will also remove any protein which is now no longer contained in any protein complex.

### Note

The entries of unwantedComplex must be found in the column names of ISI, otherwise, they will not be removed. This is especially important since there are many id's that index the same protein complex.

### Author(s)

T. Chiang

### Examples

    #mips = getMipsInfo()
    #go = getGOInfo()
    #mipsM = createMipsMatrix(mips)
    #goM = createGOMatrix(go)
    #mips2go = runCompareComplex(mipsM, goM, byWhich = "ROW")
    #merged = mergeBGMat(mipsM, goM, mips2go$toBeRm)
    #ISI = unWantedComp(merged)

[Package ScISI version 1.10.0 Index]