miRNATargetRegionsBiomart_ENSEMBL: Creates a track of miRNA target regions from ENSEMBL

Description Usage Arguments Value Author(s) References Examples

View source: R/BiofeatureGraphics.R

Description

Creates a track of miRNA target regions from ENSEMBL using the Gviz bioconductor package.

Usage

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miRNATargetRegionsBiomart_ENSEMBL(gen, chr, start, end, showId=FALSE, datasetEnsembl = "hsapiens_mirna_target_feature")

Arguments

gen

The name of the genome. Currently only handles human data from either the previous version, GRCh37 (also known as hg19) or the current version, GRCh38 (also known as hg38).

chr

The chromosome of interest

start

The starting position in the region of interest (the smallest value)

end

The end position in the region of interest (the largest value)

showId

Show the ID of the genetic elements

datasetEnsembl

Allows the user to manually set which data set is used if required.Default=hsapiens_mirna_target_feature

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to ENSEMBLregulation binding motif biomart

Examples

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library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 1000000
end <- 20000000


if(interactive()){
 miRNATargetRegionsBiomartTrack<-miRNATargetRegionsBiomart_ENSEMBL(gen,chr,start,end,
                                      datasetEnsembl = "hsapiens_mirna_target_feature")
  plotTracks(miRNATargetRegionsBiomartTrack, from = start, to = end)
} else {
  data(miRNATargetRegionsBiomartTrack)
  plotTracks(miRNATargetRegionsBiomartTrack, from = start, to = end)
}

coMET documentation built on Nov. 23, 2017, 2:05 a.m.