downloadProteinAnnotation: Download protein annotation

In nishuai/Temp: RBDmap

Description

Download a whole organism protein sequence database and sequence features from Interpro, Uniprot, and compute disorderdness and sequence complexity.

Usage

downloadProteinAnnotation(organism = "HUMAN",
                          maindatadir = ".",
                          ProtFeaturesFile = "ProtFeatures.rda",
                          RBDmapFTfile = "RBDmapFT.rda",
                          UniprotVersionFile = "UniprotVersion.rda",
                          idmappingfile,
                          fastafile)

Arguments

organism	The name of the organism. One out of ARATH, CAEEL, CHICK, DANRE, DROME, HUMAN, RAT, YEAST
maindatadir	The directory for output files.
ProtFeaturesFile	Output file for protein features used for mRNA-interactome capture.
RBDmapFTfile	Output file for protein features with protein position used by RBDmap.
UniprotVersionFile	Outputfile containing version information of Uniprot and Interpro.
idmappingfile	Unused. Will be filled according to organism.
fastafile	Unused. Will be filled according to organism.

Details

Protein sequence database is downloaded from Uniprot as well as Uniprot sequence features and Interpro domains. Disorderdned is computed by iupred and sequence complexity by the function getComplexity.

Value

Nothing is returned, but the function as a site effect the function saves the three files ProtFeaturesFile, RBDmapFTfile and UniprotVersionFile.

Warning

The download can take up to several hours to be completed.

Author(s)

Bernd Fischer

Examples

## downloadProteinAnnotation("YEAST")

nishuai/Temp documentation built on May 16, 2019, 8:12 p.m.