RFAM_sto_to_ct: A that converts a RFAM formatted sto file to a connectivity...

In JPSieg/R2easyR: Facilitates Mapping Experimental RNA Reactivity Data to Secondary Structures Drawn with R2R

A that converts a RFAM formatted sto file to a connectivity (CT) table file

Description

Parses a RFAM formatted Stockholm alignment file, pulls out the sequence you want, and maps the consensus secondary structure onto a connectivity table (CT).

Usage

RFAM_sto_to_ct(
  Path.to.sto,
  RNA.name,
  Output.name = "RNA",
  Remove.non.canonical = TRUE,
  Keep.pknots = TRUE
)

Arguments

Path.to.sto	Path to the sto file that you want to reformat
RNA.name	Name of the RNA that you want to pull out
Output.name	Prefix you want to put on the output CT file. Default = "RNA". Can be a path to a CT file storage directory.
Remove.non.canonical	Do you want to remove non canonical and non GU wobble pairs produced from the consensus allignment. Default = TRUE. Set to Remove.non.canonical = FALSE.
Keep.pknots	Do you want to keep pknots? Default = TRUE. Set to Keep.pknots = FALSE to remove pknots.

JPSieg/R2easyR documentation built on March 2, 2024, 8:42 a.m.