open_motifdb {TRN.builder} R Documentation

open the motif database

Description

Usage

open_motifdb(file);

Arguments

file

the motif database source:

  1. a directory path that contains a set of the MEME format motif files (*.meme), then a MEMEMotifRepository object will be created from this directory;

  2. a file path or a file stream object of the binary motif database file, then the database will be opened from the given data stream in read only mode.

env

[as Environment]

Details

NOTE: the db parameter of the motif_search api requires a SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.PWMDatabase object, but this function returns a MEMEMotifRepository or a SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif.PWMDatabase object, so the database object that is created by this api can not be consumed by the motif_search api directly at this moment.

Authors

TRNtoolkit

Value

a motif database object for get the position weight matrix data of each transcription factor family, which could be used by the motif_search api for run the TFBS motif site scan;

this function returns a R# error message object if the given motif database file can not be opened for read.

clr value class

Examples

[Package TRN.builder version 1.0.0.0 Index]