interestGenes_ENSEMBL {coMET} | R Documentation

## Create one track of the genes in the genomic regions of interest from EMSEMBL

### Description

Create one track of the genes in the genomic regions of interest from EMSEMBL using the Gviz bioconductor package

### Usage

    interestGenes_ENSEMBL(gen, chr, start, end, interestfeatures,interestcolor,
    showId=FALSE,title="genes (ENSEMBL)")

### Arguments

`gen` | the name of the genome
`chr` | the chromosome of interest
`start` | the first position in the region of interest (the smallest value)
`end` | the last position in the region of interest (the largest value)
`interestfeatures` | A data frame with 3 columns: start of features, end of features, and type of features
`interestcolor` | A list with the color for each new features defined
`showId` | Show the ID of the genetic elements
`title` | Name of tracks

### Value

A BiomartGeneRegionTrack object of Gviz

### Author(s)

Tiphaine Martin

### References

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

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=ensGene

### See Also

`ISCA_UCSC`, `GWAScatalog_UCSC`, `knownGenes_UCSC`, `genesName_ENSEMBL`, `GeneReviews_UCSC`, `GAD_UCSC`, `xenorefGenes_UCSC`, `transcript_ENSEMBL`,

### Examples

    library("Gviz")
    gen <- "hg19"
    chr <- "chr15"
    start <- 75011669
    end <- 75019876
    interestfeatures <- rbind(c("75011883","75013394","bad"),c("75013932","75014410","good"))
    interestcolor <- list("bad"="red", "good"="green")

    if(interactive()) {
      interestgenesENSMBLtrack<-interestGenes_ENSEMBL(gen,chr,start,end,
      interestfeatures,interestcolor,showId=TRUE)
      plotTracks(interestgenesENSMBLtrack, from = start, to =end)
    } else {
      data(interestgenesENSMBLtrack)
      plotTracks(interestgenesENSMBLtrack, from = start, to =end)
    }

[Package coMET version 1.16.0 Index]