get.operon.start.points

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

fwd.sh.incs

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

rev.sh.incs

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

Maximum acacepted start transcription level.

max.start.transc

Minimum expression level for the coding sequence regions (CDSs).

minExprCDS

verbose


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.start.points: Determine operon start-points (OSPs).

Description

Usage

Arguments