createIGVtrack: Create a junction track for IGV visualization of interection

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.