export.igraph: Export interactions to an igraph object
In LTLA/fugi: Further Utilities for Genomic Interactions
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Exports a GenomicInteractions object to graph object for use by igraph package.
This uses unique anchors as nodes and generates edges between them.
For the resulting graph to be easily interpretable, anchors should be non-overlapping.
This should already be the case for HiC data using either binned genomic regions or restriction fragments.
However, ChIA-PET data can contain overlapping anchors, which may need to be reduced to non-overlapping regions before graph export.
Usage
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export.igraph(GIObject)
## S4 method for signature 'GenomicInteractions'
export.igraph(GIObject)
Arguments
GIObject
A GenomicInteractions object.
Value
A graph representation of the GenomicInteractions object.
Author(s)
Malcolm Perry, Elizabeth Ing-Simmons
Examples
1
2
3
data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)
ig <- export.igraph(hic_example_data)
LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
Exports a GenomicInteractions object to graph object for use by igraph package. This uses unique anchors as nodes and generates edges between them.
For the resulting graph to be easily interpretable, anchors should be non-overlapping. This should already be the case for HiC data using either binned genomic regions or restriction fragments. However, ChIA-PET data can contain overlapping anchors, which may need to be reduced to non-overlapping regions before graph export.
Usage
1 2 3 4 | export.igraph(GIObject)
## S4 method for signature 'GenomicInteractions'
export.igraph(GIObject)
|
Arguments
GIObject |
A GenomicInteractions object. |
Value
A graph representation of the GenomicInteractions object.
Author(s)
Malcolm Perry, Elizabeth Ing-Simmons
Examples
1 2 3 | data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)
ig <- export.igraph(hic_example_data)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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