prepareProteome: prepare proteome for background building

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

Description

prepare proteome from UniProt webserver or a fasta file

Usage

prepareProteome(source, fasta, species = "unknown", ...)

Arguments

source	An object of UniProt.ws or A character "UniProt".
fasta	fasta file name or an object of AAStringSet
species	an character to assign the species of the proteome
...	parameters could be passed to prepareProteomeByFTP.

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 <- prepareProteome(UniProt.ws, species="Drosophila melanogaster")
 }

dagLogo documentation built on Dec. 5, 2020, 2 a.m.