compile.confirmed.operons: Compile a set of coinfirmed operons.

Description

Test the correlation coefficient beween a segment of coverage depth and a vector of 100 integers modeling a simple shape of sharp increases (or decreases) in transcription: x =[0..0,1..1] (or x =[1..1,0..0]).

Usage

compile.confirmed.operons(genes.and.operons, transcCDSs, transcIGRs.pos, transcIGRs.neg, POSSs, POESs, minExprCDS = 0.1, minExprIGR = 0.25, max.start.transc = c(0.1, 0.1), max.end.transc = c(0.1, 0.1), verbose = TRUE, ...)

Arguments

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.

POSSs

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

POESs

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

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.

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.

verbose

Default logical value is TRUE.