calculate.PFN: PFN calculation
In songw01/MEGENA: Multiscale Clustering of Geometrical Network

calculate.PFN

R Documentation

PFN calculation

Description

main function to calculate PFN a ranked list of edge pairs

Usage

calculate.PFN(edgelist,max.skipEdges = NULL,maxENum = NULL,doPar = FALSE,
	num.cores = NULL, keep.track = TRUE, save.vertex.names=TRUE,
	vertex.names.file='vertex.names.RData')
resume.calculate.PFN(edgelist, net, max.skipEdges = NULL, doPar = FALSE,
	num.cores = NULL, keep.track = TRUE, vertex.names.file='vertex.names.RData')

Arguments

`edgelist`	three column edgelist: first two columns are topological edges, and the third column is the weight. Must be a data.frame object.
`max.skipEdges`	Maximum number of edges to be searched by planarity test without any inclusion to PFN. If set NULL, it will be automatically set to number of cores x 1000. It acts as a threhold to quicken PFN construction termination during PCP.
`maxENum`	maximum number of edges to include in final PFN. Default value is NULL, which invokes maximal number of edges allowed in planar network.
`doPar`	TRUE/FALSE logical variable to choose parallelization.
`num.cores`	number of cores to use in parallelization.
`keep.track`	If TRUE, pfg_el.RData will be created in working folder. This file can be used later for restart in case PFN construction did not finish successfully. Default is TRUE.
`net`	a data.frame with intermediate network edges from a PFN job. The edges should have been converted to numeric index of vector `vertex.names` given by `vertex.names.file`.
`save.vertex.names`	whether to save vertex names that matches the gene indices in intermediate output.
`vertex.names.file`	file to save vertex names if `save.vertex.names` is `TRUE`.

Details

If doPar = TRUE, then num.cores are registered for PCP.

Value

output is three column edgelist data.frame, third column being the weight.

Author(s)

Won-Min Song

Examples

# test simplest case of planar network (a 3-clique).
a <- c(1,1,2);b <- c(2,3,3);w <- runif(3,0,1);
el <- cbind(a,b,w);el <- as.data.frame(el[order(el[,3],decreasing = TRUE),])
calculate.PFN(edgelist = el,max.skipEdges = Inf,doPar = FALSE,num.cores = NULL)

songw01/MEGENA documentation built on Jan. 19, 2024, 6:51 p.m.