predict_topology: Predict the topology of a membrane protein

In richelbilderbeek/tmhmm: Interface to TMHMM

Predict the topology of a membrane protein

Description

Predict the topology of a membrane protein

Usage

predict_topology(
  fasta_filename,
  folder_name = get_default_tmhmm_folder(),
  temp_topology_filename = tempfile(fileext = ".top")
)

Arguments

fasta_filename	path to a FASTA file
folder_name	superfolder of TMHMM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_tmhmm_folder
temp_topology_filename	filename to temporarily save the topology. This file will be deleted when this function completed successfully

Value

a tibble with the columns 'name' and 'topology', where the 'name' column hold all the proteins' names, and 'topology' contains all respective topologies.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_tmhmm_installed()) {
  fasta_filename <- system.file("extdata", "tmhmm.fasta", package = "tmhmm")
  predict_topology(fasta_filename)
}

richelbilderbeek/tmhmm documentation built on Sept. 3, 2022, 5:14 p.m.