prepareProteomeByFTP {dagLogo} | R Documentation

## 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` | 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)

[Package dagLogo version 1.25.0 Index]