detect.sid.points: Find strat/end transcription points.

In CONDOP: Condition-Dependent Operon Predictions

Description

Internal function to identify the boundaries of transcriptionally active regions using a sliding window algorithm. The sliding window algorithm uses fixed windows with a length of 100 nt that slides across the coverage-depth data table and finds segments of coverage depth highly and statistically correlated with 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

detect.sid.points(cd, sizeWindow, verbose = TRUE)

Arguments

cd	A data table containing the coverage depth of an RNA-seq expression profile(s).
sizeWindow	An annotation data table.
verbose

Details

With default values, segments having a positive correlation coefficient (exceeding 0.7) and a significant correlation test p-value (<10-7) are selected. are slected. The vector of the sliding window of 100 integers is a good trade-off between the accuracy of sharp increases/decreases in transcription and the computational costs of the procedure. P-value 10-7 allows reliable identification of sharp increases/decreases in transcription.

Author(s)

Vittorio Fortino detect.sid.points()

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