RNAfold: Invoke RNAfold

In RachelSilverstein/BioTools: Tools for bio computing

Description

Input RNA sequences to be analyzed by RNAfold.

Usage

RNAfold(RNAs, options = "--noPS -p --jobs='0'")

Arguments

RNAs	Character vector of RNA sequences to be analyzed. A DNA sequence is also ok... T will be converted to U.
options	Additional parameters to pass to RNAfold. Default is "–noPS -p –jobs='0'". (Calculates partition function and MFE structure). Warning: always use –noPS!

Details

Pass a character vector of RNA sequences to be analyzed (and optional additional parameters for RNA fold). Returns the output of RNA fold in string format. Make sure to always keep the option –noPS. This funciton will also create dot.ps in the project directory (a dot plot). It will only create a single file if multiple inputs are supplied and continuously overwrite it. I don't want it to write this file but I can't seem to figure out how to turn it off, so the funcion jsut deletes this file before returning. Note, RNAfold must be saved in /usr/local/bin/.

Value

The output of RNAfold as a character string.

Author(s)

Rachel Silverstein (aut)

Examples

RNAfold(c("AAAAUAUUUUUUUAUAUAUUUUUUUAAAAAAA", "CCCCCTTTTTCTATTTTAAAAAAAAUUUUUU"))

RachelSilverstein/BioTools documentation built on May 3, 2019, 8:34 p.m.