| {TRN.builder} | R# Documentation |
require(GCModeller);
#' tools for create a transcription regulation network
imports "TRN.builder" from "TRNtoolkit";
tools for create a transcription regulation network
This R# package module provides the toolkit for build the transcription regulation network(TRN) from the regulon database and the motif site scan result:
open_motifdb: open the position weight matrix(PWM) motif database;
motif_search: scan the TF binding site(TFBS) motif site on the given promoter/upstream sequence regions;
regulation.footprint: create the regulation footprint(regulation network edges) from the regulator mapping data(bbh), the motif site data and the regprecise regulon database;
read.regulations/write.regulations: read and save the regulation footprint data table;
read.footprints: read the motif site(footprint site) table data.
| open_motifdb | open the motif database |
| motif_search | scan the TF binding site motif on the given sequence regions |
| read.footprints | read a footprint site model data file |
| read.regulations | read a regulation prediction result file |
| write.regulations | save the regulation network data file. |
| regulation.footprint | create the regulation footprint(regulation network edges) from the regulator mapping data, the motif site data and the regprecise regulon database |