get.operon.start.points: Determine operon start-points (OSPs).

Description Usage Arguments Author(s)

Description

Internal function to estimate the gene-level expression values using the RPKM method.

Usage

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get.operon.start.points(fwd.sh.incs, rev.sh.incs, genes.and.operons, igrs.p,
  igrs.n, transcCDSs, borders = c(100, 10), max.start.transc = c(0.1, 0.1),
  minExprCDS = 0.1, verbose = TRUE, ...)

Arguments

fwd.sh.incs

Data table containing information on the sharp increases in transcription found on the forward strand. See detect.sid.points.

rev.sh.incs

Data table containing information on the sharp increases in transcription found on the reverse strand. See detect.sid.points.

genes.and.operons

Data table merging gene(s) and operon(s) annotations.

igrs.p

Data table containing generic information of the intergenic regions on the forward strand. See get.intergenic.regions.

igrs.n

Data table containing generic information of the intergenic regions on the reverse strand. See get.intergenic.regions.

transcCDSs

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

borders

A vector.

max.start.transc

Maximum acacepted start transcription level.

minExprCDS

Minimum expression level for the coding sequence regions (CDSs).

verbose

Author(s)

Vittorio Fortino get.operon.start.points()



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