Description Usage Arguments Details Value Author(s)

View source: R/PFN_Computation.R

PFN construction by parallelized edge screening.

1 2 | ```
compute.PFN.par(sortedEdge,Ng,maxENum,Njob,Ncore,max.skipEdges = NULL,
keep.track = TRUE,initial.links = NULL)
``` |

`sortedEdge` |
3-column matrix for the input edgelist (e.g. - correlation pair list). Must be sorted by third column, which is usually weight vector. |

`Ng` |
integer. number of genes included in sortedEdge. |

`maxENum` |
Maximum number of edges to include in final PFN. The theoretical maximal number enforced by Euler's formula is 3(Ng-2). |

`max.skipEdges` |
Maximum number of edges to be counted before any valid edge to be included in PFN. This works as a termination condition to avoid exhaustive planarity testing over all edges provided in sortedEdge. |

`Njob` |
Number of edges to be passed to each core for parallelized edge screening. |

`Ncore` |
Number of cores to utilize. |

`keep.track` |
TRUE/FALSE logical. Indicate if the record of PFN construction is saved in temporary file "pfg_el.RData". Default is TRUE. |

`initial.links` |
If provided, PFN construction will restart by regarding these initial.links as already-built PFN. |

This is parallelized implementation of PFN construction, where it is possible to re-capture PFN construction by providing already computed edgelist into initial.links. Although provivded, this function itself may require careful caution and users are encouraged to use more user-friendly "calculate.PFN()" instead.

A 3-column matrices, where first two columns are integer indices for vertices, and third is the weight vector.

Won-Min Song

MEGENA documentation built on May 29, 2017, 12:33 p.m.

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