GetShortestPath {MACPET} | R Documentation |
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.
GetShortestPath(object, ...) ## Default S3 method: GetShortestPath(object, ...) ## S3 method for class 'GenomeMap' GetShortestPath(object, threshold = NULL, ChrFrom, ChrTo, SummitFrom, SummitTo, ...)
object |
An object of class |
... |
Further arguments to be passed to |
threshold |
A numeric with the FDR cut-off threshold used to take a
subset of significant interactions If |
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. |
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
.
Ioannis Vardaxis, ioannis.vardaxis@ntnu.no
Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Complete pipeline for ChIA-PET. To be published.
#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)