getUniprotData: getUniprotData

In BIMSBbioinfo/slimR: Short Linear Motif (SLiM) Analysis in the context of human diseases

Description

Batch download different types of proteome-wide annotation data from Uniprot using REST services

Usage

getUniprotData(outDir, format, reviewed = TRUE, organism = 9606,
  update = FALSE)

Arguments

outDir	Target download folder path
format	File format. Accepted formats are gff, fasta, txt
reviewed	Only download reviewed uniprot entries (default: TRUE)
organism	Organism code e.g. 9606 for human
update	Boolean (default: FALSE), whether to download updated annotations to the target folder

Value

Path to the downloaded file

Examples

#download Tobacco Rattle Virus proteome (it has only 6 genes)
#https://www.uniprot.org/proteomes/UP000001669
up <- getUniprotData(outDir = getwd(), format = 'fasta',
                    reviewed = TRUE, organism = 652939)
up_fasta <- Biostrings::readAAStringSet(up)
## Not run: 
#download gff annotation for human reviewed proteome
gffFile <- getUniprotData(outDir = getwd(), format = 'fasta',
                    reviewed = TRUE, organism = 9606)
gff <- rtracklayer::import.gff(gffFile)

## End(Not run)

BIMSBbioinfo/slimR documentation built on Nov. 4, 2021, 6:48 a.m.