get_topology: Get a topology as a tibble.

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Get a topology as a tibble.

Description

Topologyies are downloaded and stored at the user's data folder

Usage

get_topology(
  target_name = "human",
  proteome_type = "full",
  keep_selenoproteins = TRUE,
  topology_prediction_tool,
  data_folder = rappdirs::user_data_dir(appname = "bbbq"),
  verbose = FALSE
)

Arguments

target_name	abbreviated name of organism or virus. Use get_target_names to get the valid values. Use get_target_english_name to get the English name of a target.
proteome_type	type of proteome, must be either full or representative
keep_selenoproteins	keep the selenoproteins. The reason to discard these, is that TMHMM cannot deal with selenoproteins.
topology_prediction_tool	tool to predict the topology of a membrane protein. Possible values are: mhcnuggetsr pureseqtmr, which uses PureseqTM mhcnuggetsr tmhmm, which uses TMHMM
data_folder	folder where BBBQ stores its data, such as proteomes and prediced topologies.
verbose	set to TRUE for more output

richelbilderbeek/bbbq documentation built on July 27, 2023, 2:15 a.m.