## ----setup, include = FALSE-------------------------------------------------------------------------------------------
options(width=120)
knitr::opts_chunk$set(
   collapse = TRUE,
   eval=interactive(),
   echo=TRUE,
   comment = "#>"
)

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
# library(igvR)
# igv <- igvR()
# setBrowserWindowTitle(igv, "Paired-end demo")
# setGenome(igv, "hg38")
# tbl.bedpe <- data.frame(chrom1=c("2","2"),
#                         start1=c(105780000, 105575000),
#                         end1=c(105790000, 105600000),
#                         chrom2=c("2","2"),
#                         start2=c(105890000, 106075000),
#                         end2=c(105900000, 106100000),
#                         stringsAsFactors=FALSE)
# 
#   # construct a "region of interest" (roi) string from tbl.bedpe
#   # this is where our two features are found.
# 
# shoulder <- 300000
# roi <- sprintf("%s:%d-%d", tbl.bedpe$chrom1[1],
#                            min(tbl.bedpe$start1) - shoulder,
#                            max(tbl.bedpe$end2) + shoulder)
# 
# showGenomicRegion(igv, roi)
# track <- BedpeInteractionsTrack("ENCFF110BUX", tbl.bedpe)
# displayTrack(igv, track)

## ----eval=TRUE, echo=FALSE, out.width="95%"---------------------------------------------------------------------------
knitr::include_graphics("pairedEnd.png")

## ----eval=TRUE--------------------------------------------------------------------------------------------------------
sessionInfo()