getCondOperonMap

Data table containing the POPs predicted as OPs.

pred.POPs

Data table containing the DOPs predicted as OPs.

pred.DOPs

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

genes.and.operons

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

POSSs

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

POESs

Add gene pairs predicted as OPs to confirmed operons.

find.ext

Save the condition-dependent operon map in a BED-like file.

BED.file

Save the condition-dependent operon map in a tab-delimited text file file.

TAB.file

verbose

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


Build the condition-dependent operon map for a given RNA-seq expression profile.


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.

getCondOperonMap: Build the condition-dependent operon map for a given RNA-seq expression profile.

Description

Usage

Arguments