## ----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, "H3K4Me3 GATA2") # setGenome(igv, "hg38") # showGenomicRegion(igv, "GATA2") # zoomOut(igv) # zoomOut(igv) ## ----eval=TRUE, echo=FALSE, out.width="95%"--------------------------------------------------------------------------- knitr::include_graphics("images/gata2-63kb.png") ## ----eval=FALSE------------------------------------------------------------------------------------------------------- # getGenomicRegion(igv) ## ----eval=TRUE, echo=FALSE, out.width="95%"--------------------------------------------------------------------------- knitr::include_graphics("images/ucscTableBrowser.png") ## ----eval=TRUE, echo=FALSE, out.width="95%"--------------------------------------------------------------------------- knitr::include_graphics("images/ucscTableBrowserOutput.png") ## ----eval=TRUE, echo=FALSE, out.width="95%"--------------------------------------------------------------------------- knitr::include_graphics("images/ucscTableBrowser-getOutput.png") ## ----eval=FALSE------------------------------------------------------------------------------------------------------- # tbl <- read.table("~/drop/k562-h3k4me3-gata2.tsv", sep="\t", skip=1, as.is=TRUE, fill=TRUE) # colnames(tbl) <- c("chrom", "start", "end", "score") ## ----eval=FALSE------------------------------------------------------------------------------------------------------- # lapply(tbl, class) ## ----eval=FALSE------------------------------------------------------------------------------------------------------- # track <- DataFrameQuantitativeTrack("H3K4Me3 K562", tbl, autoscale=TRUE, color="darkGreen") # displayTrack(igv, track) ## ----eval=TRUE, echo=FALSE, out.width="95%"--------------------------------------------------------------------------- knitr::include_graphics("images/gata2-63kb-h3k4me3.png") ## ----eval=TRUE-------------------------------------------------------------------------------------------------------- sessionInfo()