Description Usage Arguments Value Author(s) References See Also Examples
View source: R/GetShortestPath-methods.R
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.
1 2 3 4 5 6 7 8 9 10 11 12 | 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, ...)
|
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.
1 2 3 4 5 6 7 8 9 | #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)
|
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