miRNATargetRegionsBiomart_ENSEMBL: Creates a track of miRNA target regions from ENSEMBL

In TiphaineCMartin/coMET_original: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

Description

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

Usage

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

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)
}

TiphaineCMartin/coMET_original documentation built on May 9, 2019, 4:49 p.m.