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

In CONDOP: Condition-Dependent Operon Predictions

Description

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

Usage

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()

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