getDataFiles: getDataFiles
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 many helper functions to compute the cluster lists, functional module, and edge weights and then sends the data to CSV files so that it can be output by Cytoscape.

1	getDataFiles(SData, Ps)

`SData`	A Seurat object containing preprocessed data
`Ps`	Pvalues containing the Pvalues for each gene in the clusters
`cnames`	A list containing names for each of the clusters. Defaults to NULL and uses C1, C2... instaed

Does not return any variable. Creates 2 CSV files for every cluster. One for the nodes and another for the edges in Cytoscape.

calls getClusterList, getFM, getEdgeWeightsF, and SendToCSV

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.

getDataFiles(SData = seqwell, Ps = PValues)

## The function is currently defined as
function (SData, Ps) 
{
    countTable <- SData[["RNA"]]@data
    CList <- getClusterList(SData, Ps)
    FMList <- list()
    i = 0
    for (c in CList) {
        pValues <- c$p_val
        names(pValues) <- c$gene
        FMList[[paste("FM", as.character(i), sep = "")]] <- FM(pValues)
        i = i + 1
    }
    networkList <- list()
    i = 0
    for (f in FMList) {
        networkList[[paste("N", as.character(i), sep = "")]] <- getEdgeWeights(f, 
            countTable)
        i = i + 1
    }
    i = 1
    nClusters <- length(CList)
    while (i <= nClusters) {
        SendToCSV(FMList[[i]], networkList[[i]], CList[[i]], 
            (i - 1))
        i = i + 1
    }
  }