GetShortestPath: Find shortest path between pairs of peaks given a set of...

In MACPET: Model based analysis for paired-end data

Description

GetShortestPath function subsets the significant interactions of a GenomeMap object given a user specified FDR cut-off. Based on the leftover interactions, it creates a network and finds the length of the shortest path between two user-specified peaks. Currently it only finds the shortest paths between intra-chromosomal peaks. Therefore, the peaks have to be on the same chromosome.

Usage

GetShortestPath(object, ...)

## Default S3 method:
GetShortestPath(object, ...)

## S3 method for class 'GenomeMap'
GetShortestPath(object, threshold = NULL, ChrFrom,
  ChrTo, SummitFrom, SummitTo, ...)

## S4 method for signature 'GenomeMap'
GetShortestPath(object, threshold = NULL, ChrFrom,
  ChrTo, SummitFrom, SummitTo, ...)

Arguments

object	An object of class GenomeMap.
...	Further arguments to be passed to GetShortestPath (not used).
threshold	A numeric with the FDR cut-off threshold used to take a subset of significant interactions If threshold=NULL then all the interactions will be used
ChrFrom	Character specifying the chromosome of the 'From' peak, for example 'chr1'.
ChrTo	Character specifying the chromosome of the 'To' peak.
SummitFrom	Numeric specifying the peak summit of the 'From' peak.
SummitTo	Numeric specifying the peak summit of the 'To' peak.

Value

A two-element list with the first element named LinearPathLength for the linear length of the path between SummitFrom and SummitTo, and the second element named ThreeDPathLength for the 3D length of the shortest path between SummitFrom and SummitTo.

Author(s)

Ioannis Vardaxis, [e-mail]

References

Vardaxis I, Drabl<c3><b8>s F, Rye M and Lindqvist BH (2018). MACPET: Complete pipeline for ChIA-PET. To be published.

See Also

GenomeMap

Examples

#load Interaction data: (class=GenomeMap)
load(system.file('extdata', 'MACPET_GenomeMapData.rda', package = 'MACPET'))
class(MACPET_GenomeMapData)
GetShortestPath(object=MACPET_GenomeMapData,
                    threshold = NULL,
                    ChrFrom='chr1',
                    ChrTo='chr1',
                    SummitFrom=10000,
                    SummitTo=1000000)

MACPET documentation built on Nov. 8, 2020, 5:47 p.m.