export.chiasig: Export interactions in a BEDPE-like format for use with...
In LTLA/fugi: Further Utilities for Genomic Interactions
Description
Usage
Arguments
Value
Author(s)
References
Examples
Description
Exports a GenomicInteractions object to file in a BEDPE-like format for use with ChiaSig.
Usage
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export.chiasig(GIObject, fn = NULL, score = "counts")
## S4 method for signature 'GenomicInteractions'
export.chiasig(GIObject, fn = NULL,
score = "counts")
Arguments
GIObject
A GenomicInteractions object.
fn
String containing a path to a file to write the interaction data to.
score
String or integer scalar specifying the metadata column to export as the score field.
Value
If fn is supplied, NULL is invisibly returned and a file is created at fn.
Otherwise, a data.frame is returned containing all of the corresponding information from GIObject.
Author(s)
Malcolm Perry, Elizabeth Ing-Simmons
References
Paulsen et al. (2014).
A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions.
Nucleic Acids Res. 42(18), e143.
Examples
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data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)
export.chiasig(hic_example_data, fn = tempfile(), score = "counts")
LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.
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Description Usage Arguments Value Author(s) References Examples
Description
Exports a GenomicInteractions object to file in a BEDPE-like format for use with ChiaSig.
Usage
1 2 3 4 5 | export.chiasig(GIObject, fn = NULL, score = "counts")
## S4 method for signature 'GenomicInteractions'
export.chiasig(GIObject, fn = NULL,
score = "counts")
|
Arguments
GIObject |
A GenomicInteractions object. |
fn |
String containing a path to a file to write the interaction data to. |
score |
String or integer scalar specifying the metadata column to export as the |
Value
If fn is supplied, NULL is invisibly returned and a file is created at fn.
Otherwise, a data.frame is returned containing all of the corresponding information from GIObject.
Author(s)
Malcolm Perry, Elizabeth Ing-Simmons
References
Paulsen et al. (2014). A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. Nucleic Acids Res. 42(18), e143.
Examples
1 2 3 | data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)
export.chiasig(hic_example_data, fn = tempfile(), score = "counts")
|
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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