select.pops: Define a set of gene pairs POPs with an "operon status" to (re)define represent used to train the operon classifier.

Description

Internal function to build a data table containing gene pairs and the correspoding transcriptomic/genomic feature values. The operon classifier trained/validated on the OPs and NOPs is used to predict the operon status of these gene pairs.

Usage

select.pops(OPs, NOPs, genes.and.operons, transcCDSs, transcIGRs.pos, transcIGRs.neg, minExprCDS = 0.1, minExprIGR = 0.25, maxLenIGR = 150, POSSs, POESs, max.start.transc, max.end.transc, wseq, verbose = TRUE, ...)

Arguments

OPs

Data table including the confirmed operon pairs (OPs). See select.ops.

genes.and.operons

Data table merging gene(s) and operon(s) annotations. See join.genes.and.operons.

transcCDSs

Transcription levels for the coding regions. See comp.gene.transc.levels.

transcIGRs.pos

Transcription levels for the intergenic regions (forard strand). See comp.igr.transc.levels.

transcIGRs.neg

Transcription levels for the intergenic regions (reverse strand). See comp.igr.transc.levels.

minExprCDS

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

minExprIGR

Minimum expression level for the intergenic regions (IGRs). Default values is 0.25.

maxLenIGR

Maximum length for the intergenic regions (IGRs). Default values is 150.

POSSs

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

POESs

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

max.start.transc

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

max.end.transc

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

wseq

Sequence genome.

verbose

Default logical value is TRUE.

OPs

Data table including the confirmed non-operon pairs (NOPs). See select.nops.