## ---- echo=FALSE-------------------------------------------------------------- # These settings make the vignette prettier knitr::opts_chunk$set(results="hold", collapse=FALSE, message=FALSE) #refreshPackage("GenomicDistributionsData") #devtools::build_vignettes("code/GenomicDistributionsData") #devtools::test("code/GenomicDistributionsData") ## ----echo=TRUE, results="hide", message=FALSE, warning=FALSE------------------ library(GenomicDistributionsData) library(ExperimentHub) ## ---- ExpHub-Obj-------------------------------------------------------------- hub = ExperimentHub() query(hub, "GenomicDistributionsData") ## ----chrom-sizes-------------------------------------------------------------- # Retrieve the chrom sizes file c = hub[["EH3473"]] head(c) ## ----chrom-sizes-meta--------------------------------------------------------- # Access the chrom sizes file and inspect its metadata chromSizes = query(hub, c("GenomicDistributionsData", "chromSizes_hg38")) chromSizes ## ----chrom-sizes-alt, eval=FALSE---------------------------------------------- # # Retrieve the chromosome sizes file from ExperimentHub # c2 = chromSizes[[1]] ## ----Transcription-Start-Sites------------------------------------------------ TSS = hub[["EH3477"]] TSS[1:3, "symbol"] ## ----gene-models-------------------------------------------------------------- #GeneModels = buildGeneModels("hg38") GeneModels = hub[["EH3481"]] # Get the locations of exons head(GeneModels[["exonsGR"]]) ## ----open-signal-matrix, eval=FALSE------------------------------------------- # #hg38OpenSignal = buildOpenSignalMatrix("hg38") # OpenSignal = hub[["EH3485"]] # head(OpenSignal) ## ----load-data-by-name, eval=FALSE-------------------------------------------- # chromSizes_hg38() # chromSizes_hg19() # chromSizes_mm10() # chromSizes_mm9() # TSS_hg38() # TSS_hg19() # TSS_mm10() # TSS_mm9() # geneModels_hg38() # geneModels_hg19() # geneModels_mm10() # geneModels_mm9() # openSignalMatrix_hg38() # openSignalMatrix_hg19() # openSignalMatrix_mm10()