filterBYmotifType: Filter ELM database motif occurrence GRanges by motif type
In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
Filter ELM database motif occurrence GRanges by motif type
Usage
1
2
filterBYmotifType(instances, motif_types = c("DOC", "MOD", "LIG", "DEG",
"CLV", "TRG"))
Arguments
instances
ELM database motif occurrence GRanges object returned by ELMdb2GRanges
motif_types
character vector of motif types
Value
Genomic Ranges object filtered by motif type (ELMType column)
Author(s)
Vitalii Kleshchevnikov
See Also
SLIMFinderOcc2GRanges, GRangesINinteractionSubsetFASTA
Examples
1
2
3
instances9606 = ELMdb2GRanges(dbfile = "../viral_project/data_files/instances9606.gff",
dburl = "http://elm.eu.org/instances.gff?q=None&taxon=Homo%20sapiens&instance_logic=")
instances9606 = filterBYmotifType(instances9606, motif_types = c("DOC", "MOD", "LIG", "DEG", "CLV", "TRG"))
vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
Description
Filter ELM database motif occurrence GRanges by motif type
Usage
1 2 | filterBYmotifType(instances, motif_types = c("DOC", "MOD", "LIG", "DEG",
"CLV", "TRG"))
|
Arguments
instances |
ELM database motif occurrence GRanges object returned by |
motif_types |
character vector of motif types |
Value
Genomic Ranges object filtered by motif type (ELMType column)
Author(s)
Vitalii Kleshchevnikov
See Also
SLIMFinderOcc2GRanges, GRangesINinteractionSubsetFASTA
Examples
1 2 3 | instances9606 = ELMdb2GRanges(dbfile = "../viral_project/data_files/instances9606.gff",
dburl = "http://elm.eu.org/instances.gff?q=None&taxon=Homo%20sapiens&instance_logic=")
instances9606 = filterBYmotifType(instances9606, motif_types = c("DOC", "MOD", "LIG", "DEG", "CLV", "TRG"))
|
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