createIGVtrack {ELMER} | R Documentation |
Create a junction track for IGV visualization of interection
createIGVtrack( pairs, met.platform = "450K", genome = "hg38", filename = "ELMER_interactions.bed", color.track = "black", track.name = "junctions", gene.symbol = NULL, all.tss = TRUE )
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). |
Tiago Chedraoui Silva (tiagochst at gmail.com)
## 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)