# #——回声= FALSE -------------------------------------------------------------- 配置< -系统。文件(“extdata”、“config.csv”、包=“amplican”)配置<——read.csv(配置)knitr:: kable(头(配置 )) ## ---- configPath,呼应= TRUE, eval = FALSE ---------------------------------------- # 系统。文件(“extdata”、“config.csv”,包= " amplican ") ## ---- amplicanPipeline,呼应= TRUE, eval = FALSE ---------------------------------- # # 路径#配置< -系统配置文件示例。File ("extdata"， "config.csv"， package = "amplican") # #到示例fastq文件的路径# fastq_folder <- system. csv"文件(“extdata”,包=“amplican”)# #输出文件夹,完整路径# results_folder < - tempdir() # # #运行amplican # amplicanPipeline(配置、fastq_folder results_folder) # # #的结果分析可以发现#消息(results_folder ) ## ---- 回声= FALSE -------------------------------------------------------------- barcodeFilters < -系统。文件(“extdata”、“结果”,“barcode_reads_filters.csv”,包=“amplican”)barcodeFilters <——read.csv (barcodeFilters) knitr:: kable(头(barcodeFilters )) ## ---- 回声= FALSE -------------------------------------------------------------- config_summary < -系统。文件(“extdata”、“结果”,“config_summary.csv”,包=“amplican”)config_summary < - read.csv (config_summary) config_summary <——config_summary [c(“ID”,“条形码”、“读”、“Reads_Filtered”、“Reads_In”、“Reads_Del”、“Reads_Edited”、“Reads_Frameshifted”)]knitr:: kable(头(config_summary )) ## ---- 回声= TRUE --------------------------------------------------------------- # 路径例子RunParameters.txt run_params < -系统。文件(“extdata”、“结果”,“RunParameters.txt”,包=“amplican”)#文件readline (run_params的显示内容 ) ## ---- 回声= TRUE, eval = FALSE --------------------------------------------------- # # #系统路径例子比对文件夹。文件(“extdata”,“结果”、“对齐”,包= " amplican ") ## ---- 回声= FALSE -------------------------------------------------------------- 比对< -系统。文件(“extdata”,“结果”、“对齐”,“events_filtered_shifted_normalized.csv”,包=“amplican”)比对<——read.csv(校准)knitr:: kable(头(对齐 )) ## ---- 回声= TRUE --------------------------------------------------------------- < -系统。文件("extdata"， "results"， "alignments"， "AlignmentsExperimentSet. "rds"， package = "amplican") aln <- readRDS(aln) amplican::lookupAlignment(aln, ID = "ID_1") #将打印ID_1的最频繁对齐