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

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
#  library(igvR)
#  library(AnnotationHub)
#  
#  igv <- igvR()
#  setBrowserWindowTitle(igv, "H3K27ac GATA2")
#  setGenome(igv, "hg19")
#  showGenomicRegion(igv, "GATA2")
#  for(i in 1:4) zoomOut(igv)

## ----eval=TRUE, echo=FALSE, out.width="95%"---------------------------------------------------------------------------
knitr::include_graphics("images/annotationHub-01.png")

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
#  aHub <- AnnotationHub()
#  query.terms <- c("H3K27Ac", "k562")
#  length(query(aHub, query.terms))  # found 7
#  h3k27ac.entries <- query(aHub, query.terms)

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
#  x.broadPeak <- aHub[["AH23388"]]
#  x.bigWig <- aHub[["AH32958"]]

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
#  roi <- getGenomicRegion(igv)
#  gr.broadpeak <- x.broadPeak[seqnames(x.broadpeak)==roi$chrom &
#                              start(x.broadpeak) > roi$start &
#                              end(x.broadpeak) < roi$end]

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
#  names(mcols(gr.broadpeak))
#    #  "name"        "score"       "signalValue" "pValue"      "qValue"
#  mcols(gr.broadpeak) <- gr.broadpeak$score
#  track <- GRangesQuantitativeTrack("h3k27ac bp", gr.broadpeak, autoscale=TRUE, color="brown")
#  displayTrack(igv, track)

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
#  
#  file.bigWig <- resource(x.bigWig)[[1]]
#  gr.roi <- with(roi, GRanges(seqnames=chrom, IRanges(start, end)))
#  gr.bw <- import(file.bigWig, which=gr.roi, format="bigWig")
#  track <- GRangesQuantitativeTrack("h3k27ac.bw", gr.bw, autoscale=TRUE, color="gray")
#  displayTrack(igv, track)
#  

## ----eval=TRUE, echo=FALSE, out.width="95%"---------------------------------------------------------------------------
knitr::include_graphics("images/annotationHub-02.png")

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