getFM: getFM
In mheffe3/SCNVC: Generates Single Cell Networks that can be used in Cytoscape

Description Usage Arguments Value Note Author(s) Examples

View source: R/SCRNA.R

Calls scPPIN functions to compute a steiner tree that finds the best solution to the connections in a cluster from the single cell data and returns it in functional module object. Called by getDataFiles

1	getFM(pvalues)

pvalues

A vector containing the named pvalues for each node in a cluster

Returns a functional module containing the solution to the connections of the ppi network solved by dapcstp

Called by getDataFiles and getCyGraphs

Matt Heffernan, University of Illinois at Chicago

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

getFM(pValues)

## The function is currently defined as
function (pvalues) 
{
    ppin <- loadPPIN()
    checksum = sum(pvalues < 0) + sum(pvalues > 1)
    if (checksum > 0) {
        warning("p-values are not in (0,1]!")
    }
    FDR <- 10^{
        -2
    }
    pvalues[pvalues < 10^-308] <- 10^-308
    functionalModule <- detectFunctionalModule(ppin, pvalues, 
        FDR)
    return(functionalModule)
  }