ELMdb2GRanges: Download and read ELM database motif occurrences

In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference

Description

Download and read ELM database motif occurrences

Usage

ELMdb2GRanges(dbfile = "../viral_project/data_files/instances9606.gff",
  dburl = "http://elm.eu.org/instances.gff?q=None&taxon=Homo%20sapiens&instance_logic=",
  tsvurl = "http://elm.eu.org/instances.tsv?q=None&taxon=Homo%20sapiens&instance_logic=",
  tsvfile = "../viral_project/data_files/instances9606.tsv")

Arguments

dbfile	a path to a gff (txt) file containing ELM database motif occurrences
dburl	url where to get ELM database containing motif occurrences

Details

ELM database containing motif occurrences in human proteins (9606): "http://elm.eu.org/instances.gff?q=None&taxon=Homo

ELM database containing motif occurrences in viral proteins (10239): "http://elm.eu.org/instances.gff?q=all&taxon=irus&instance_logic="

Value

Genomic Ranges object containing ELM database motif occurrences

Author(s)

Vitalii Kleshchevnikov

See Also

SLIMFinderOcc2GRanges, GRangesINinteractionSubsetFASTA

Examples

instances9606 = ELMdb2GRanges(dbfile = "../viral_project/data_files/instances9606.gff",
                  dburl = "http://elm.eu.org/instances.gff?q=None&taxon=Homo%20sapiens&instance_logic=")
instances10239 = ELMdb2GRanges(dbfile = "../viral_project/data_files/instances10239.gff",
                  dburl = "http://elm.eu.org/instances.gff?q=all&taxon=irus&instance_logic=")

vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.