simulate: Simulate reactivity

In yub18/DESSERT: Differential Analysis of RNA Structure Probing Experiments at Nucleotide Resolution: Uncovering Regulatory Functions of RNA Structure

Simulate reactivity

Description

Given RNA sequences, this function simulates reactivity accounting for multiple structural conformations and dependencies between adjacent nucleotide positions.

Usage

simulate(
  seq,
  dir_ViennaRNA,
  types,
  ncores = "auto",
  plot_cor = FALSE,
  clear = TRUE
)

Arguments

seq	List of RNA sequences.
dir_ViennaRNA	Directory of ViennaRNA software. See Details.
types	Vector of reactivity types ('icSHAPE', 'Cordero' and 'Sokusd' supported).
ncores	Number of cores for parallel computation. Automatically determined by default.
plot_cor	Logical value indicating whether to plot within/between group correlations.
clear	Logical value indicating whether to clear intermediate files.

Details

Users need to have ViennaRNA software installed to simulate structural conformations from sequences.

Value

A list containing the following components:

r	Simulated reactivity.
stru	A list of simulated structural conformations.
truth	A list of vectors indicating positions of structurally variable regions.
w	Weights of dominant conformations.

yub18/DESSERT documentation built on Nov. 5, 2024, 2:36 a.m.