searchMotif: Search motif PFM and beta score matrix (if source is...

In benoukraflab/TFregulomeR: TFregulomeR reveals transcription factors’ context-specific features and functions

Search motif PFM and beta score matrix (if source is MethMotif) for a given TFregulomeR ID in TFregulomeR

Description

This function allows you to obtain motif PFM matrix and beta score matrix (if source is MethMotif) for a given TFregulomeR ID in TFregulomeR

Usage

searchMotif(
  id,
  motif_format = "MEME",
  server = "ca",
  TFregulome_url,
  local_db_path = NULL
)

Arguments

id	Required. TFregulomeR ID.
motif_format	Motif PFM format, either in MEME by default or TRANSFAC.
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

MethMotif class object

Examples

K562_CEBPB <- searchMotif(id = "MM1_HSA_K562_CEBPB")
K562_CEBPB_transfac <- searchMotif(id = "MM1_HSA_K562_CEBPB",
                                   motif_format = "TRANSFAC")

benoukraflab/TFregulomeR documentation built on July 8, 2024, 5:03 p.m.