## ----echo=FALSE, out.width='30%',fig.align='center'--------------------------- knitr::include_graphics('./logo.png') ## ----setup, echo=FALSE, results="hide"---------------------------------------- knitr::opts_chunk$set(tidy = FALSE, cache = FALSE, dev = "png", message = FALSE, error = FALSE, warning = TRUE) vigDir=getwd() if(dir.exists("../inst/extdata")){ knitr::opts_knit$set(root.dir = "../inst/extdata") }else{ knitr::opts_knit$set(root.dir = "../extdata") } ## ----message=FALSE, warning=FALSE,eval=FALSE---------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("OGRE") ## ----message=FALSE, warning=FALSE--------------------------------------------- library(OGRE) ## ----InitializeOGRE, message=TRUE, echo=TRUE,warning=FALSE-------------------- myQueryFolder <- file.path(system.file('extdata', package = 'OGRE'),"query") mySubjectFolder <- file.path(system.file('extdata', package = 'OGRE'),"subject") myOGRE <- OGREDataSetFromDir(queryFolder=myQueryFolder, subjectFolder=mySubjectFolder) ## ----checkMetadata, message=TRUE, echo=TRUE,warning=TRUE---------------------- metadata(myOGRE) ## ----loadAnnotations, message=TRUE, echo=TRUE,warning=TRUE-------------------- myOGRE <- loadAnnotations(myOGRE) ## ----checkDatasetNames, message=TRUE, echo=TRUE,warning=TRUE------------------ names(myOGRE) ## ----checkGRanges, message=TRUE, echo=TRUE,warning=TRUE----------------------- myOGRE ## ----echo=FALSE, out.width='70%',fig.align='center'--------------------------- knitr::include_graphics(file.path(vigDir,'overlap.png')) ## ----fOverlaps, message=TRUE, echo=TRUE,warning=TRUE-------------------------- myOGRE <- fOverlaps(myOGRE) head(metadata(myOGRE)$detailDT,n=2) ## ----sumPlot, echo=TRUE, message=TRUE, warning=TRUE,fig.dim = c(30/2.54, 20/2.54)---- myOGRE <- sumPlot(myOGRE) metadata(myOGRE)$barplot_summary ## ----gvizPlot, message=TRUE, echo=TRUE,warning=FALSE-------------------------- myOGRE <- gvizPlot(myOGRE,"ENSG00000142168",showPlot = TRUE, trackRegionLabels = setNames(c("name","name"),c("genes","CGI"))) ## ----summarizeOverlap, message=TRUE, echo=TRUE,warning=FALSE------------------ myOGRE <- summarizeOverlap(myOGRE) myOGRE <- plotHist(myOGRE) metadata(myOGRE)$summaryDT metadata(myOGRE)$hist$TFBS ## ----coveragePlot, message=TRUE, echo=TRUE,warning=FALSE---------------------- myOGRE <- covPlot(myOGRE) metadata(myOGRE)$covPlot$TFBS$plot ## ----datasetsFromAnnotationHub,eval=FALSE------------------------------------- # myOGRE <- OGREDataSet() # listPredefinedDataSets() # myOGRE <- addDataSetFromHub(myOGRE,"protCodingGenes","query") # myOGRE <- addDataSetFromHub(myOGRE,"CGI","subject") # myOGRE <- addDataSetFromHub(myOGRE,"TFBS","subject") # names(myOGRE) ## ----datasetsUserGRanges,eval=FALSE------------------------------------------- # myOGRE <- OGREDataSet() # myGRanges <- makeExampleGRanges() # myOGRE <- addGRanges(myOGRE,myGRanges,"query") ## ----additionalAnnotationHub,eval=FALSE--------------------------------------- # aH <- AnnotationHub() # aH[["AH5086"]] # q <- query(aH, c("GRanges","Homo sapiens", "CpG")) ## ----addgff,eval=FALSE-------------------------------------------------------- # myOGRE <- OGREDataSetFromDir(queryFolder = "pathToQueryFolder", # subjectFolder = "pathToSubjectFolder") # myOGRE <- loadAnnotations(myOGRE) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()