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

In linquynus/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 = "sg", TFregulome_url)

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 "http://bioinfo-csi.nus.edu.sg/methmotif/" or "http://methmotif.org", please use a new url.

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")

linquynus/TFregulomeR documentation built on April 27, 2022, 5:01 a.m.