select.nops

Data table merging gene(s) and operon(s) annotations. See <code>join.genes.and.operons</code>.

genes.and.operons

Data table including the confirmed operon pairs (OPs). See <code>select.ops </code>.

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

transcCDSs

Transcription levels for the intergenic regions (forard strand). See <code>comp.igr.transc.levels</code>.

transcIGRs.pos

Transcription levels for the intergenic regions (reverse strand). See <code>comp.igr.transc.levels</code>.

transcIGRs.neg

Data table representing a set of putative operon start-points.

POSSs

Data table representing a set of putative operon end-points.

POESs

wseq

Cutoff values for the start transcription points. Default values is 0.1.

max.start.transc

Cutoff values for the end transcription points. Default values is 0.1.

max.end.transc

verbose


Build a data table containing confirmed non-operon pairs (NOPs) and the feature values.


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.

select.nops: Define a set of NOPs which is used to train the operon classifier.

Description

Usage

Arguments