# # # R代码从装饰图案的ReQON来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:风格# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # BiocStyle::乳胶()# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:ReQON。Rnw: 46 - 54岁# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(ReQON)库(seqbias)图书馆(Rsamtools) reads_fn <系统。文件(“额外/例子。bam”,包= " seqbias”) #排序bam排序<——sortBam (reads_fn, tempfile()) #指数bam indexBam(排序)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:ReQON。Rnw: 67 - 88 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ref_fn < -系统。文件(“额外/例子。足总”,包= " seqbias”) ref_f < - FaFile (ref_fn)开放。FaFile (ref_f) seq < - scanFa (ref_f) len < -长度(seq [[1]]) ref < -矩阵(nrow = len ncol = 3) #染色体/序列的名字在第一列ref[1] < -代表(“seq1”, len) #序列在第2列ref [2] < - c (1: len) #在第三列str引用基地< - toString (subseq (seq [[1]], 1, len)) s < - strsplit (str, NULL) ref [3] < - s[[1]] #查看参考文件参考[1:5,]#保存参考文件编写。表(ref,文件= " ref_seq。txt”, 9 = " \ t”,引用= FALSE, row.names = FALSE, col.names = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:ReQON。Rnw: 109 - 117 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #设置培训地区reg < -粘贴(“seq1:1——“莱恩,9 = " ")诊断< - ReQON (Recalibrated_example排序。”bam”地区= reg RefSeq = " ref_seq。txt”, nerr = 20, nraf = 0.25, plotname = " Recalibrated_example_plots。pdf”) #删除参考序列文件分开(“ref_seq。txt”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:ReQON。Rnw: 148 - 153 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #显示错误计数的阅读位置诊断ReadPosErrors #美元情节ReadPosErrorPlot(诊断ReadPosErrors美元,startpos = 0) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:ReQON。Rnw: 164 - 166 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #情节QualFreqPlot (QualFreqBefore美元诊断,诊断QualFreqAfter美元)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:ReQON。Rnw:188-200 ################################################### # report FWSE from ReQON output diagnostics$FWSE # plot before recalibration and report FWSE f1 <- FWSEplot(diagnostics$ErrRatesBefore, diagnostics$QualFreqBefore, col = "blue", main_title = "Reported vs. Empirical Quality: Before") f1 # plot after recalibration and report FWSE f2 <- FWSEplot(diagnostics$ErrRatesAfter, diagnostics$QualFreqAfter, col = "red", main_title = "Reported vs. Empirical Quality: After") f2