prepareProteomeByFTP: Create an object of 'Proteome' Class.

In jianhong/dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Create an object of Proteome Class.

Description

Create an object of Proteome Class by downloading a whole proteome data from UniProt for a given organism of an NCBI taxonomy ID or species' scientific name, or by using peptide sequences in a fasta file.

Usage

prepareProteomeByFTP(
  source = "UniProt",
  taxonID = NULL,
  species = NULL,
  destDir = tempdir(check = TRUE),
  fastaFile,
  ...
)

Arguments

source	A character vector of length 1 or NULL. A database source from which the proteome sequences are to be downloaded. By default, currently it is "UniProt". If it is NULL, then fastaFile has to be specified. The priority of source is higher than fastaFile.
taxonID	An integer(1), specifying Taxonomy ID for a species of interest. Check the NCBI taxonomy database: https://www.ncbi.nlm.nih.gov/taxonomy or the UniProt database http://www.uniprot.org/taxonomy/. At least one of the two parameters, taxonID and species, should be specified. If both are specified, taxonID will be used preferentially.
species	A character vector of length 1. The Latin name of a species confirming to the Linnaean taxonomy nomenclature system. CAUTION: for species with different strains, attention should be paid. You can interactively choose the right taxonID from an output list.
destDir	A character vector of length 1. A destination directory with writing permission for saving downloaded sequences. Default is a temporary directory in the system's temporary directory.
fastaFile	A character vector of length 1. A fasta file name from which protein sequences are read in.
...	other parameters passing to the function download.file.

Value

An object of Proteome

Author(s)

Haibo Liu

Examples

## Not run: 
## Prepare an objecto of Proteome Class for a proteome from the UniProt database
#' proteome <- prepareProteomeByFTP(source = "UniProt", species = "Homo sapiens")

## End(Not run)
## Prepare an objecto of Proteome Class from a fasta file
fasta <- system.file("extdata", "HUMAN.fasta", package="dagLogo")
proteome <- prepareProteomeByFTP(source = NULL, species = "Homo sapiens", 
fastaFile=fasta)

jianhong/dagLogo documentation built on June 8, 2025, 2:07 a.m.