CyFilter: CyFilter
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

Filters the Cytoscape graph to include only NodeScores > NSLB OR EdgeWeights > |0.05| Then creates a subnetwork from it

1	CyFilter(FM, name, NSLB = 100, EWLB = 0.05)

`FM`	functional module from scPPIN
`name`	name of FM cluster
`NSLB`	Lower bound for Node Score filtering
`EWLB`	Lower Bound For Edge Weight filtering

No return value simply outputs a subnetwork to Cytoscape

Requires Cytoscape to be opened and installed. Called by 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.

CyFilter <- function(FM=FM0, name="endothelial", NSLB = 100, EWLB = 0.05)

## The function is currently defined as
function(FM, name, NSLB = 100, EWLB = 0.05)
{
  createColumnFilter(filter.name="Node Score Filter", column = "nodeScore", c(NSLB, max(V(FM0)$nodeScore)), predicate = "BETWEEN")
  createColumnFilter(filter.name = "Edge Weight Filter", column = "weight", c(-EWLB, EWLB), predicate = "IS_NOT_BETWEEN", type = "edges")
  createCompositeFilter(filter.name = "Edge Weight & Node Score Filter", c("Node Score Filter", "Edge Weight Filter"), "ANY")
  createSubnetwork(subnetwork.name = paste(name, "Filtered Network", sep=""))
  
}