## ----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()