# # # R代码从装饰图案来源的啪嗒啪嗒地响。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:自由# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(触发器)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 2号代码块:数据# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据。文件< -执行文件。路径(“extdata”、“vignette-sam.txt”),包=“触发器”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:estim # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #最小数量的集群读#考虑一群读基因(默认40):min.read < - 50 #的minimim跨越数读#考虑有效结min.junc = 10 #亚型的最大数量给#在正规化道路(默认10):max。iso < - 7 ff。res < -啪嗒啪嗒地响(data.file =数据。文件,out.file = ' FlipFlop_output。gtf’, minReadNum = min。阅读,minJuncCount = min。接合,max_isoforms = max.iso) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:名字# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #名称(ff.res) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:输出# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #记录< - ff。res成绩单美元[[1]]abundancesFPKM < - ff。res abundancesFPKM美元[[1]]的预期。计数< - ff.res美元的预期。重要的[[1]]打印(成绩单)打印(abundancesFPKM)打印(expected.counts) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:annot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # annot。文件< -执行文件。路径(“extdata”、“vignette-annot.bed.txt”),包=“触发器”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:estim_annot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ff.res。annot < -啪嗒啪嗒地响(data.file =数据。文件,out.file = ' FlipFlop_output。gtf’, annot.file = annot.file) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:output_annot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #记录。annot < - ff.res。annot$transcripts[[1]] print(transcripts.annot) ################################################### ### code chunk number 9: GenomicFeatures ################################################### if(require(GenomicFeatures)){ txdb <- makeTranscriptDbFromGFF(file='FlipFlop_output.gtf', format='gtf', exonRankAttributeName='exon_number') # List of exons for each transcript: exonsBy(txdb, by='tx') } ################################################### ### code chunk number 10: sessionInfo ################################################### sessionInfo()