## ----style, echo = FALSE, results = 'asis'--------------------------------- BiocStyle::markdown() ## ---- message=FALSE-------------------------------------------------------- library(Chicago) library(PCHiCdata) ## -------------------------------------------------------------------------- dataPath <- system.file("extdata", package="PCHiCdata") testDesignDir <- file.path(dataPath, "hg19TestDesign") dir(testDesignDir) ## -------------------------------------------------------------------------- testDataPath <- file.path(dataPath, "GMchinputFiles") dir(testDataPath) files <- c( file.path(testDataPath, "GM_rep1.chinput"), file.path(testDataPath, "GM_rep2.chinput"), file.path(testDataPath, "GM_rep3.chinput") ) ## -------------------------------------------------------------------------- settingsFile <- file.path(system.file("extdata", package="PCHiCdata"), "sGM12878Settings", "sGM12878.settingsFile") ## ---- message=FALSE-------------------------------------------------------- library(Chicago) cd <- setExperiment(designDir = testDesignDir, settingsFile = settingsFile) ## ---- message=FALSE-------------------------------------------------------- cd <- readAndMerge(files=files, cd=cd) ## ---- eval=FALSE----------------------------------------------------------- # cd <- chicagoPipeline(cd) ## ---- echo=FALSE, message=FALSE-------------------------------------------- cd <- chicagoPipeline(cd) ## -------------------------------------------------------------------------- outputDirectory <- tempdir() exportResults(cd, file.path(outputDirectory, "vignetteOutput")) ## ----echo=FALSE------------------------------------------------------------ a <- read.table(file.path(outputDirectory, "vignetteOutput.ibed"), header=TRUE) head(a) ## ----echo=FALSE------------------------------------------------------------ a <- read.table(file.path(outputDirectory, "vignetteOutput_seqmonk.txt"), header=FALSE) head(a) ## ----echo=FALSE------------------------------------------------------------ a <- read.table(file.path(outputDirectory, "vignetteOutput_washU_text.txt"), header=FALSE) head(a) ## ----eval=FALSE------------------------------------------------------------ # # plottedBaitIDs <- plotBaits(cd, n=6) # ## ----echo=FALSE, fig.height=10--------------------------------------------- invisible(plotBaits(cd, baits=c(415839, 404491, 425847, 417632, 409335, 414114))) ## -------------------------------------------------------------------------- featuresFolder <- file.path(dataPath, "GMfeatures") dir(featuresFolder) featuresFile <- file.path(featuresFolder, "featuresGM.txt") featuresTable <- read.delim(featuresFile, header=FALSE, as.is=TRUE) featuresList <- as.list(featuresTable$V2) names(featuresList) <- featuresTable$V1 featuresList ## ---- message=FALSE, fig.width=12, fig.height=7---------------------------- no_bins <- ceiling(max(abs(intData(cd)$distSign), na.rm = TRUE)/1e4) enrichmentResults <- peakEnrichment4Features(cd, folder=featuresFolder, list_frag=featuresList, no_bins=no_bins, sample_number=100) ## -------------------------------------------------------------------------- enrichmentResults ## ---- message=FALSE-------------------------------------------------------- library(GenomicInteractions) library(GenomicRanges) gi <- exportToGI(cd) ## ---- message=FALSE-------------------------------------------------------- library(AnnotationHub) ah <- AnnotationHub() hs <- query(ah, c("GRanges", "EncodeDCC", "Homo sapiens", "H3k4me1")) enhancerTrack <- hs[["AH23254"]] ## -------------------------------------------------------------------------- otherEnds <- anchorTwo(gi) otherEnds <- renameSeqlevels(otherEnds, c("chr20","chr21")) ## -------------------------------------------------------------------------- findOverlaps(otherEnds, enhancerTrack) ## -------------------------------------------------------------------------- hs["AH23254"]$genome ## -------------------------------------------------------------------------- head(intData(cd), 2) ## -------------------------------------------------------------------------- newCd = copyCD(cd) ## -------------------------------------------------------------------------- weightsPath <- file.path(system.file("extdata", package="Chicago"), "weights") dir(weightsPath) ## ---- message=FALSE-------------------------------------------------------- weightSettings <- file.path(weightsPath, "GM12878-2reps.settings") cd <- setExperiment(designDir = testDesignDir, settingsFile = weightSettings) ## -------------------------------------------------------------------------- sessionInfo()