# #——style-knitr eval = TRUE,呼应= FALSE,结果= '飞机 '-------------------- BiocStyle:乳胶 () ## ---- 包括= FALSE --------------------------------------------------------- 库(knitr) opts_chunk美元设置(和谐= TRUE ) ## ---- 包括= FALSE --------------------------------------------------------- 库(knitr) opts_chunk美元设置(和谐= TRUE ) ## ---- =“隐藏”选项,结果,消息= FALSE, eval = TRUE,回声= FALSE ---------------------- 库(breakpointR)选项(宽度= 90)# # - eval = FALSE ------------------------------------------------------------------------- # 运行库(breakpointR) # # # breakpointR缺省参数# breakpointR (inputfolder =“folder-with-BAMs”,outputfolder = '输出文件夹 ') ## ---- eval = TRUE -------------------------------------------------------------------------- ? breakpointr # # - eval = FALSE ------------------------------------------------------------------------- # breakpointr(…breakpointR.config configfile =” ') ## ---- eval = FALSE ------------------------------------------------------------------------- # callHotSpots = TRUE # # - eval = TRUE,消息= FALSE ----------------------------------------------------------- 库(breakpointR) # #得到一些示例文件datafolder < -系统。file("extdata"， "example_bams"， package="breakpointRdata") outputfolder <- tempdir() ##执行breakpointR breakpointR (inputfolder = datafolder, outputfolder = outputfolder，染色体= 'chr22'， pairedEndReads =FALSE，重用. exists .files =FALSE, windowsize = 1000000, binMethod = 'size'， pair2frgm =FALSE, min.mapq = 10, filtAlt = TRUE) ## ----eval=FALSE------------------------------------------------------------------------- # breakpointR(…min.mapq = 10, filtAlt = TRUE) # #——eval = FALSE ------------------------------------------------------------------------- # 库(breakpointR) # # #装箱策略基于期望本长度# breakpointR (inputfolder = folder-with-BAM, outputfolder =“输出文件夹”,# windowsize = 1 e6, binMethod =“大小”)# # #装箱策略基于用户定义的读每一本# breakpointR (inputfolder = folder-with-BAM, outputfolder =“输出文件夹”,# windowsize = 100,binMethod = '读取 ') ## ---- eval = TRUE,警告= FALSE,消息= FALSE -------------------------------------------- ## 例子deltaW值exampleFolder < -系统。file("extdata"， "example_results"， package="breakpointRdata")[1]断点。对象< - loadFromFiles (exampleFile)头(breakpoint.object[[1]]美元三角洲)# # - eval = FALSE ------------------------------------------------------------------------- # ## 断点运行使用的主要热点分析breakpointR函数# breakpointR(…callHotSpots = TRUE) # # - eval = TRUE,消息= FALSE ----------------------------------------------------------- ## 使用导出的数据断点运行热点分析exampleFolder < -系统。file("extdata"， "example_results"， package="breakpointRdata")files(exampleFolder, full.names=TRUE)断点。objects <- loadFromFiles(exampleFiles) ##提取断点坐标break <- lapply(breakpoint. properties)objects， '[['， 'breaks') ##获取热点坐标hotspot <- hotspotter(breaks, bw=1e6) ## ----eval=TRUE, warning=FALSE, message=FALSE, fig.width=12, fig.height=4---------------- ##绘制单个库exampleFolder <- system. properties。file("extdata"， "example_results"， package="breakpointRdata")files(exampleFolder, full.names=TRUE)[1] plotBreakpoints(exampleFile) ## ----eval=TRUE, warning=FALSE, message=FALSE, fig.width=12, fig.height=5---------------- ## Plotting a single library exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata") exampleFiles <- list.files(exampleFolder, full.names=TRUE)[1:4] plotBreakpointsPerChr(exampleFiles, chromosomes = 'chr7') ## ----sessionInfo, results='asis', eval=TRUE--------------------------------------------- toLatex(sessionInfo())