imprintedGenes_GTEx {coMET} | R Documentation

## 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, 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)
    }

[Package coMET version 1.16.0 Index]