selectNuclPos: Function to compute selections of nucleotide positions.

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

Function to compute selections of nucleotide positions.

Description

This function selects pairs of nucleotide positions for computing log-ratios of control-control and treatment-control replicate comparisons.

Usage

    selectNuclPos(se, Nc, Nt, 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. selectNuclPos uses the assays "coverage" and "dropoff_count".
Nc	Number of control experimental replicates. Must be at least 2.
Nt	Number of treatment experimental replicates. Must be at least 2.
t	Threshold for the minimum allowed coverage. Must be non-negative.

Details

This function uses combn.

Value

analysedC	List where each element corresponds to a control-control replicate comparison. Each element holds indices of nucleotides that have coverage >= t and a drop-off count > 0 in both replicates of that comparison.
analysedCT	List where each element corresponds to a treatment-control replicate comparison. Each element holds indices of nucleotides that have coverage >= t and a drop-off count > 0 in both replicates of that comparison.

Error

The following errors are returned if:

"The number of experimental replicates must be at least 2." the number of control or treatment experimental replicates is less than 2;

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

"The coverage and drop-off count matrices should not have NA entries." the coverage and drop-off count matrices have NA entries.

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

    selectNuclPos(se, 3, 3, 1)

alinaselega/BUMHMM documentation built on March 2, 2024, 10 p.m.