toTFBSTools: convert motif PFM in TFregulomeR into PFMatrix class object...

View source: R/toTFBSTools.R

toTFBSToolsR 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 July 8, 2024, 5:03 p.m.