# #——风格,回声= FALSE,结果= '飞机 '------------------------------- BiocStyle:减价 () ## ---- 消息= FALSE ------------------------------------------------------ 库(芝加哥)库(PCHiCdata ) ## ------------------------------------------------------------------------ dataPath公司< -系统。testDesignDir <- file. file("extdata"， package="PCHiCdata")路径(dataPath公司,“hg19TestDesign”)dir (testDesignDir ) ## ------------------------------------------------------------------------ testDataPath < -文件。path(dataPath， "GMchinputFiles") dir(testDataPath) files <- c(file. path， "GMchinputFiles")testDataPath， "GM_rep1.chinput")，文件。testDataPath， "GM_rep2.chinput")，文件。路径(GM_rep3.chinput testDataPath。 ") ) ## ------------------------------------------------------------------------ settingsFile < file.path(系统。文件(“extdata”,包=“PCHiCdata”),“sGM12878Settings”、“sGM12878.settingsFile ") ## ---- 消息= FALSE ------------------------------------------------------ 库(芝加哥)cd < setExperiment (designDir = testDesignDir settingsFile = settingsFile ) ## ---- 消息= FALSE ------------------------------------------------------ cd < - readAndMerge(文件=文件,cd = cd ) ## ---- eval = FALSE --------------------------------------------------------- # cd < - chicagoPipeline (cd ) ## ---- 呼应= FALSE,消息= FALSE ------------------------------------------ cd < - chicagoPipeline (cd ) ## ------------------------------------------------------------------------ outputDirectory < - tempdir () exportResults (cd,文件。路径(vignetteOutput outputDirectory。 ")) ## ---- 回声= FALSE ---------------------------------------------------------- < - read.table(文件。路径(outputDirectory vignetteOutput.ibed),头= TRUE)头(a) # #——回声= FALSE ---------------------------------------------------------- < - read.table(文件。路径(outputDirectory vignetteOutput_seqmonk.txt),头= FALSE)头(a) # #——回声= FALSE ---------------------------------------------------------- < - read.table(文件。路径(outputDirectory vignetteOutput_washU_text.txt),头= FALSE)头(a) # # - eval = FALSE ---------------------------------------------------------- # # plottedBaitIDs < plotBaits (cd, n = 6 ) # ## ---- 回声= FALSE, fig.height = 10 ------------------------------------------- 看不见(plotBaits (cd,鱼饵= c (415839, 404491, 425847, 417632, 409335, 414114 ))) ## ------------------------------------------------------------------------ featuresFolder < -文件。path(dataPath， "GMfeatures") dir(featuresFolder) featuresFile <- file. path(dataPath， "GMfeatures")path(featuresFolder， " featuresgmt .txt") featuresTable <- read.delim(featuresFile, header=FALSE, as.is=TRUE) featurelist <- as.list(featuresTable$V2) names(featuresList) <- featuresTable$V1 featuresList ## ---- message=FALSE, fig.width=12, fig.height=7-------------------------- no_bins <- ceiling(max(abs(intData(cd)$distSign)， na。rm = TRUE)/1e4) mentresults <- peakment4features (cd, folder= featresfolder, list_frag=featuresList, no_bins=no_bins，sample_number = 100 ) ## ------------------------------------------------------------------------ enrichmentResults # #——消息= FALSE ------------------------------------------------------ 图书馆(GenomicInteractions)图书馆(GenomicRanges)胃肠道< - exportToGI (cd ) ## ---- 消息= FALSE ------------------------------------------------------ 库(AnnotationHub)啊< - AnnotationHub () h < -查询(啊,c(“农庄”,“EncodeDCC”,“智人”, "H3k4me1")) enhancerTrack <- hs[["AH23254"]] ## ------------------------------------------------------------------------ otherEnds <- anchorTwo(gi) otherEnds <- renameSeqlevels(otherEnds, c("chr20","chr21")) ## ------------------------------------------------------------------------ findOverlaps(otherEnds, enhancerTrack) ## ------------------------------------------------------------------------ hs["AH23254"]$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()