## ----样式，echo = false，结果=“ asis”，cache = false，message = false ---------------------------------------------------------库（knitr）库（rmarkDown）biocStyle :: markdown（）opts_chunk $ set（图width = 14，fig.height = 10，cache = true，error = false，message，message = false）选项（digits = 4，scipen = 10，stringsasFactors = false，width = 100）#options（“ citation_format” =“ pandoc”）## ----设置，cache = false -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------库（dchiprep）库（ggplot2）库（deseq2）## ----- pythonscripts，cache = false ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- pythonscriptsdir <-system.file（“ exec”，package =“ dchiprep”）pythonscriptsdir list.files（pythonscriptsdir）## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data(exampleSampleTable) exampleSampleTable ## ---- data_import_r_py，依赖森=“采样” ------------------------------------------------------------------------------------------------------------------------------------------------------------------目录<-file.path（system.file（“ ex））tdata", package="DChIPRep")) importedData <- importData(exampleSampleTable, directory) ## ----show_imported_data, dependson="data_import_R_Py"-------------------------------------------------- importeddata deseq2data（importData）head（标准化范围（deseq2data（importeddata））））## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------依赖子=“采样” ----------------------------------------------------------------------------------------------------- data(exampleInputData) data(exampleChipData) exampleSampleTable exampleInputData[1:10, ] exampleChipData[1:10, ] imDataFromMatrices <- importDataFromMatrices(inputData = exampleInputData, chipData = exampleChipData, sampleTable = exampleSampleTable) ## ----import_soGGi，eval = false --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃＃数据（sample_table_galonska）＃data（tss_galonska）＃＃bam_dir <-file.path（system.file（“ extdata”，package）=“ dchiprep”））＃wce_bam <-“ submpled_0001_pc_srr2144628_wce_wce_bowtie2_mapped-only_xs-filt_no-dups.bam”＃mat_wcer，wce_bam），＃tss = tss_galonska，＃fragment_lengths = sample_table_galonska $ input_fragment_length [1]，＃sample_ids = sample_table_galonska $ input [1] ----perform_Tests, dependson="inspect_example_data"---------------------------------------------- imDataFromMatrices <- runTesting(imDataFromMatrices, plotFDR = TRUE) ## ----accessResults, dependson="perform_Tests"----------------------------------------------------- res <- resultsDChIPRep(imDataFromMatrices) head(res) table( res$lfdr < 0.2) ## ----plot_Sig, dependson="accessResults"---------------------------------------------------------- sigPlot <- plotSignificance(imDataFromMatrices) sigPlot ## ----plot_TSS, dependson="accessResults"---------------------------------------------------------- profilePlot <- plotProfiles(imDataFromMatrices) profilePlot ## ---- cache=FALSE--------------------------------------------------------------------------------- sessionInfo()