prepareProteome: prepare proteome for background building

Description Usage Arguments Value Author(s) See Also Examples

View source: R/prepareProteome.R

Description

prepare proteome from UniProt webserver or a fasta file

Usage

1
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

1
2
3
4
5
6
if(interactive()){
   library(UniProt.ws)
   availableUniprotSpecies("Drosophila melanogaster")
   UniProt.ws <- UniProt.ws(taxId=7227)
   proteome <- prepareProteome(UniProt.ws, species="Drosophila melanogaster")
 }

jianhong/dagLogo documentation built on Nov. 6, 2019, 9:56 a.m.