toTFBSTools: convert motif PFM in TFregulomeR into PFMatrix class object...
In benoukraflab/TFregulomeR: TFregulomeR reveals transcription factors’ context-specific features and functions
toTFBSTools R Documentation
convert motif PFM in TFregulomeR into PFMatrix class object in TFBSTools package
Description
This function allows you to retrieve and convert motif PFM in TFregulomeR database into PFMatrix class object, which can be used in TFBSTools package.
Usage
toTFBSTools(id, server = "ca", TFregulome_url, local_db_path = NULL)
Arguments
id
Required. TFregulomeR ID.
server
server localtion to be linked, either 'sg' or 'ca'.
TFregulome_url
TFregulomeR server is implemented in MethMotif server. If the MethMotif url is NO more "https://bioinfo-csi.nus.edu.sg/methmotif/" or "https://methmotif.org", please use a new url.
local_db_path
The complete path to the SQLite implementation of TFregulomeR database available at "https://methmotif.org/API_ZIPPED.zip"
Value
An object of class PFMatrix
Examples
require(TFBSTools)
CEBPB_pfm <- toTFBSTools(id = "MM1_HSA_K562_CEBPB")
benoukraflab/TFregulomeR documentation built on April 17, 2024, 7:57 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| toTFBSTools | R Documentation |
convert motif PFM in TFregulomeR into PFMatrix class object in TFBSTools package
Description
This function allows you to retrieve and convert motif PFM in TFregulomeR database into PFMatrix class object, which can be used in TFBSTools package.
Usage
toTFBSTools(id, server = "ca", TFregulome_url, local_db_path = NULL)
Arguments
id |
Required. TFregulomeR ID. |
server |
server localtion to be linked, either 'sg' or 'ca'. |
TFregulome_url |
TFregulomeR server is implemented in MethMotif server. If the MethMotif url is NO more "https://bioinfo-csi.nus.edu.sg/methmotif/" or "https://methmotif.org", please use a new url. |
local_db_path |
The complete path to the SQLite implementation of TFregulomeR database available at "https://methmotif.org/API_ZIPPED.zip" |
Value
An object of class PFMatrix
Examples
require(TFBSTools)
CEBPB_pfm <- toTFBSTools(id = "MM1_HSA_K562_CEBPB")
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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