# # # R代码从装饰图案的FilterFFPE来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:风格# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # BiocStyle::乳胶()# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:选择# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(宽度= 60)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:findArtifactChimericReads # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(FilterFFPE) #发现工件嵌合读取文件< -系统。文件(“extdata”、“例子。bam”,包= " FilterFFPE”)倒转褶皱< - tempdir () FFPEReadsFile < - paste0(倒转褶皱,/ example.FFPEReads.txt) dupChimFile < - paste0(倒转褶皱,“/ example.dupChim.txt”) artifactReads <——findArtifactChimericReads(=文件、线程= 2,FFPEReadsFile = FFPEReadsFile dupChimFile = dupChimFile)头(artifactReads) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:filterBamByReadNames # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #过滤器工件嵌合读取和PCR或光学复制嵌合读取dupChim < - readline (dupChimFile) readsToFilter < - c (artifactReads dupChim)目的地<——paste0(倒转褶皱,/ example.FilterFFPE.bam) filterBamByReadNames(=文件,readsToFilter = readsToFilter目的地=目的地,覆盖= TRUE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:FFPEReadFilter # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #执行发现文件< -系统和过滤功能。文件(“extdata”、“例子。bam”,包= " FilterFFPE”)倒转褶皱< - tempdir () FFPEReadsFile < - paste0(倒转褶皱,/ example.FFPEReads.txt) dupChimFile < - paste0(倒转褶皱,“/ example.dupChim.txt”)目的地<——paste0(倒转褶皱,/ example.FilterFFPE.bam) FFPEReadFilter(= =文件、线程= 2,目的地的目的地,覆盖= TRUE, FFPEReadsFile = FFPEReadsFile dupChimFile = dupChimFile) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:scanBAM # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #加载bam文件与scanBAM newBam < - Rsamtools:: scanBAM(目的地)头(newBam[[1]]美元seq) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:sessionInfo # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # packageDescription (FilterFFPE) sessionInfo ()