## ----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()