vignettes/pairedEnd.R

In paul-shannon/IGV: igvR: integrative genomics viewer

## ----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 <- 100000
## 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()