## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----dosetup,echo=FALSE,results="hide"---------------------------------------- suppressPackageStartupMessages({ library(rtracklayer) library(BiocStyle) library(erma) library(GenomicFiles) library(ggplot2) library(grid) library(png) library(DT) }) ## ----lkm---------------------------------------------------------------------- library(DT) library(erma) meta = mapmeta() kpc = c("Comments", "Epigenome.ID..EID.", "Epigenome.Mnemonic", "Quality.Rating", "Standardized.Epigenome.name", "ANATOMY", "TYPE") datatable(as.data.frame(meta[,kpc])) ## ----lkst--------------------------------------------------------------------- data(states_25) datatable(states_25) ## ----dofig,fig=TRUE----------------------------------------------------------- library(png) im = readPNG(system.file("pngs/emparms.png", package="erma")) grid.raster(im) ## ----getgf-------------------------------------------------------------------- ermaset = makeErmaSet() ermaset cellTypes(ermaset)[1:5] datatable(as.data.frame(colData(ermaset)[,kpc])) ## ----getgm, cache=FALSE------------------------------------------------------- uil33 = flank(resize(range(genemodel("IL33")), 1), width=50000) uil33 ## ----bind--------------------------------------------------------------------- rowRanges(ermaset) = uil33 ermaset ## ----getcss------------------------------------------------------------------- library(BiocParallel) register(MulticoreParam(workers=2)) suppressWarnings({ csstates = lapply(reduceByFile(ermaset, MAP=function(range, file) { imp = import(file, which=range, genome=genome(range)[1]) seqlevels(imp) = seqlevels(range) imp$rgb = erma:::rgbByState(imp$name) imp }), "[[", 1) }) tys = cellTypes(ermaset) # need to label with cell types csstates = lapply(1:length(csstates), function(x) { csstates[[x]]$celltype = tys[x] csstates[[x]] }) csstates[1:2] ## ----doviz, fig=TRUE---------------------------------------------------------- csProfile(ermaset[,1:5], symbol="CD28", useShiny=FALSE)