computeStretches: Function to compute continuous stretches of nucleotide...

In BUMHMM: Computational pipeline for computing probability of modification from structure probing experiment data

Description

This function computes continuous stretches of nucleotide positions, for which posterior probabilities are to be computed. Such positions should have the minimum allowed coverage (as defined with the parameter t) in all experimental replicates and a non-zero drop-off count in at least one of the treatment replicates. The returned stretches are at least two nucleotides long.

Usage

    computeStretches(se, t)

Arguments

se	A SummarizedExperiment object storing structure probing data and the associated genomic sequence. The documentation for the example data set provided with the package se outlines how the object should be defined. computeStretches uses the assays "coverage" and "dropoff_count".
t	Threshold for the minimum allowed coverage. Must be non-negative.

Value

An IRanges object storing each stretch.

Error

The following errors are returned if:

"The minumum coverage threshold must be non-negative." the threshold for the minimum considered coverage is negative.

Author(s)

Alina Selega, Sander Granneman, Guido Sanguinetti

References

Selega et al. "Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments", Nature Methods (2016).

Examples

    t <- 1
    stretches <- computeStretches(se, t)

BUMHMM documentation built on Nov. 8, 2020, 5:13 p.m.