createIGVtrack {ELMER} | R Documentation

## Create a junction track for IGV visualization of interection

### Description

Create a junction track for IGV visualization of interection

### Usage

    createIGVtrack(
      pairs,
      met.platform = "450K",
      genome = "hg38",
      filename = "ELMER_interactions.bed",
      color.track = "black",
      track.name = "junctions",
      gene.symbol = NULL,
      all.tss = TRUE
    )

### Arguments

`pairs` | A data frame output from getPairs function
`met.platform` | DNA methyaltion platform to retrieve data from: EPIC or 450K (default)
`genome` | Which genome build will be used: hg38 (default) or hg19.
`filename` | Filename (".bed")
`color.track` | A color for the track (i.e blue, red,#272E6A)
`track.name` | Track name
`gene.symbol` | Filter pairs to a single gene.
`all.tss` | A logical. If TRUE it will link probes to all TSS of a gene (transcript level), if FALSE it will link to the promoter region of a gene (gene level).

### Author(s)

Tiago Chedraoui Silva (tiagochst at gmail.com)

### Examples

     ## Not run:
    data <- ELMER:::getdata("elmer.data.example")
    nearGenes <-GetNearGenes(TRange=getMet(data)[c("cg00329272","cg10097755"),],
                             geneAnnot=getExp(data))
    Hypo.pair <- get.pair(data=data,
                           nearGenes=nearGenes,
                           permu.size=5,
                           group.col = "definition",
                           group1 = "Primary solid Tumor",
                           group2 = "Solid Tissue Normal",
                           raw.pvalue = 0.2,
                           Pe = 0.2,
                           dir.out="./",
                           label= "hypo")
     createIGVtrack(Hypo.pair,met.platform = "450K", genome = "hg38")

    ## End(Not run)

[Package ELMER version 2.14.0 Index]