prepareProteomeByUniProtWS: Prepare a Proteome object for background building

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

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")
 }

jianhong/dagLogo documentation built on Nov. 5, 2024, 7:46 a.m.