get_proteome_filename: Get the name of a proteome file

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Get the name of a proteome file

Description

Get the name of a proteome file.

Usage

get_proteome_filename(
  target_name = "human",
  proteome_type = "full",
  keep_selenoproteins = TRUE
)

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.

Details

These filename match the UniProt names, and one can use UniprotR:::GetProteomeFasta to download these. Because UniprotR does not work on a continous integration service, the proteomes are downloaded from www.richelbilderbeek.nl/[proteom_filename]

Examples

get_proteome_filename()
get_proteome_filename(target = "hiv")

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