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

In CONDOP: Condition-Dependent Operon Predictions

Description

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

Usage

select.nops(genes.and.operons, OPs, transcCDSs, transcIGRs.pos, transcIGRs.neg,
  POSSs, POESs, wseq, 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.
OPs	Data table including the confirmed operon pairs (OPs). See select.ops .
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.
wseq	Sequence genome.
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.

Author(s)

Vittorio Fortino select.nops()

CONDOP documentation built on May 2, 2019, 1:26 p.m.