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 2.12.0 Index]