coMET (version 1.4.4)

imprintedGenes_GTEx: Creates a imprinted genes track from GTEx

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)

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

Value

An AnnotationTrack object of Gviz

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(chr,start, end, tissues="all", classification="imprinted",showId=TRUE)
   StomachIGtrack <-imprintedGenes_GTEx(chr,start, end, tissues="Stomach", classification="all",showId=TRUE)
   PancreasIGtrack <- imprintedGenes_GTEx(chr,start, end, tissues="Pancreas", classification="all",showId=TRUE)
   PancreasimprintedIGtrack <- imprintedGenes_GTEx(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)
}