create the regulation footprint(regulation network edges) from the regulator

regulation.footprint {TRN.builder}

R Documentation

create the regulation footprint(regulation network edges) from the regulator

Description

mapping data, the motif site data and the regprecise regulon database

Usage

regulation.footprint(regulators, motifLocis, regprecise);

Arguments

regulators

the regulator mapping data, which can be a vector of the BestHit object(the bbh best hit mapping result of the regulator protein to the target genome), or a pipeline object that produces a set of the @T:SMRUCC.genomics.Interops.NCBI.Extensions.LocalBLAST.Application.BBH.BestHit

motifLocis

a vector of the FootprintSite motif site data, which could be loaded from a csv table file via the read.footprints api: the src property of the site data is the transcription factor family name set of the corresponding motif site and the gene. [as FootprintSite]

regprecise

the regprecise regulon database object(@T:SMRUCC.genomics.Data.Regprecise.TranscriptionFactors. [as TranscriptionFactors]

env

[as Environment]




        Details

        only the regulator of the TF type in the regprecise database will be used for create the regulation network, and the transcription factor family name of the regulator is the first token of the family data which is splitted by the / or the \ character.

the regulator mapping is created by the bbh best hit: the HitName of the BestHit data is mapped to the regprecise regulator via its locus id(the text after the last : character), and the QueryName is used as the regulator gene id in the target genome.

        
Authors

        TRNtoolkit

        Value

        a pipeline object of the RegulationFootprint regulation network edge data: each edge is a regulation of one regulator to one target gene, which is created by mapping the motif site to the regulator of the corresponding transcription factor family in the regprecise database, the duplicated edge({regulator}->{regulated}) will be removed automatically;

this function returns NULL if the given regulator mapping data is nothing, or a R# error message object if the given regulator data is not a collection of the BestHit data.
clr value class
pipeline

        Examples

        

        
        [Package TRN.builder version 1.0.0.0 Index]