get_proteome: Get a proteome as a tibble.

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Get a proteome as a tibble.

Description

Proteomes are downloaded and stored at the user's data folder.

Usage

get_proteome(
  target_name = "human",
  proteome_type = "full",
  keep_selenoproteins = TRUE,
  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.
data_folder	folder where BBBQ stores its data, such as proteomes and prediced topologies.
verbose	set to TRUE for more output

Details

The option keep_selenoproteins only has an effect for the human proteome, as it is the only proteome that contains selenocysteines.

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