prepareProteomeByUniProtWS: Prepare a Proteome object for background building

Description Usage Arguments Value Author(s) See Also Examples

View source: R/prepareProteomeByUniProtWS.R

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

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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

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

haibol2016/dagLogo documentation built on June 28, 2020, 1:31 a.m.