imprintedGenes_GTEx: Creates a imprinted genes track from GTEx

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

Description

Creates a track of imprinted genes from GTEx using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

imprintedGenes_GTEx(gen="hg19", chr,start, end, tissues="all",
classification="all",showId=FALSE, title="Imprinted genes GTEx")

Arguments

gen	the name of the genome. Default value=hg19
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)
tissues	list of tissues among 33 tissues in GTEx
classification	list of classification from 5 types (biallelic, consistent with biallelic, consistent with imprinting, imprinted, NC)
showId	logical. say if we write the name of group
title	The name of the annotation track

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

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

Got to BindingMotifsBiomart binding motif biomart

Examples

library("Gviz")
gen<-"hg19"
chr<- "chr6"
start <- 144251437
end <- 144330541


if(interactive()){
   allIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
   tissues="all", classification="imprinted",showId=TRUE)
   allimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
   tissues="all", classification="imprinted",showId=TRUE)
   StomachIGtrack <-imprintedGenes_GTEx(gen,chr,start, end,
   tissues="Stomach", classification="all",showId=TRUE)
   PancreasIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
   tissues="Pancreas", classification="all",showId=TRUE)
   PancreasimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
   tissues="Pancreas", classification="biallelic",showId=TRUE)

   imprintinglist <- list(allIGtrack,allimprintedIGtrack,
   StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack)

  plotTracks(imprintinglist, from = start, to = end)

} else {

  data(allIGtrack)
  data(allimprintedIGtrack)
  data(StomachIGtrack)
  data(PancreasIGtrack)
  data(PancreasimprintedIGtrack)

   imprintinglist <- list(allIGtrack,allimprintedIGtrack,
   StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack)

  plotTracks(imprintinglist, from = start, to = end)
}

coMET documentation built on Nov. 8, 2020, 5 p.m.