prepareProteomeByUniProtWS {dagLogo} | R Documentation

## Prepare a Proteome object for background building

### Description

Create an object of `Proteome` Class by query the UniProt database of an organism of a given species' scientific name, or by using peptide sequences in a fasta file or in an AAStringSet object.

### Usage

    prepareProteomeByUniProtWS(UniProt.ws, fasta, species = "unknown")

### Arguments

`UniProt.ws` | An object of `UniProt.ws`.
`fasta` | A fasta file name or an object of `AAStringSet`.
`species` | An character vector of length (1) to designate the species of the proteome

### Value

An object of Proteome which contain protein sequence information.

### Author(s)

Jianhong Ou

### See Also

`formatSequence`, `buildBackgroundModel`

### Examples

    if(interactive()){
       library(UniProt.ws)
       availableUniprotSpecies("Drosophila melanogaster")
       UniProt.ws <- UniProt.ws(taxId=7227)
       proteome <- prepareProteomeByUniProtWS(UniProt.ws, species="Drosophila melanogaster")
     }

[Package dagLogo version 1.26.2 Index]