fold: Fold with Sliding Windows

Description Usage Arguments Value

View source: R/fold.R

Description

Perform folding inference using sliding windows and RNAfold from the ViennaRNA Package 2.0 by Lorenz et al. doi:10.1186/1748-7188-6-26.

Usage

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fold(
  filename,
  winsize,
  stepsize,
  same_num_samples = TRUE,
  rnafold_params = "-p",
  verbose = FALSE
)

Arguments

filename

The name of the file which the sequences in FASTA format are to be read from.

winsize

Window size of the sliding windows.

stepsize

Step size of the sliding windows.

same_num_samples

If TRUE, fold will perform additional foldings at the beginning and end of the sequence. This allows the beginning and end of the sequence to have the same amount of samples/windows go through it. This is specially important for calculating Shannon's entropy.

rnafold_params

Parameters used by RNAfold. The default is '-p'.

verbose

If TRUE, fold will print information of performance.

Value

List of RNAfold results for each sliding window.


ruthkr/rnafolding documentation built on Jan. 9, 2021, 3:22 p.m.