get.operon.end.points

Data table merging gene(s) and operon(s) annotations.

genes.and.operons

Data table containing generic information of the intergenic regions on the forward strand. See <code>get.intergenic.regions</code>.

igrs.p

Data table containing generic information of the intergenic regions on the reverse strand. See <code>get.intergenic.regions</code>.

igrs.n

Transcription levels for the coding regions. See <code>comp.gene.transc.levels</code>.

transcCDSs

borders

Minimum expression level for the coding sequence regions (CDSs). Default values is 0.1.

minExprCDS

verbose

Data table containing information on the sharp decreases in transcription found on the forward strand. See <code>detect.sid.points</code>.

fwd.sh.incs

Data table containing information on the sharp decreases in transcription found on the reverse strand. See <code>detect.sid.points</code>.

rev.sh.incs

max.start.transc


Internal function to estimate the gene-level expression values using the RPKM method.


internal

An implementation of the computational strategy for the
comprehensive analysis of condition-dependent operon maps in prokaryotes
proposed by Fortino et al. (2014) <DOI:10.1186/1471-2105-15-145>.
It uses RNA-seq transcriptome profiles to improve prokaryotic operon map inference.

get.operon.end.points: Determine operon end-points (OEPs).

Description

Usage

Arguments