## ----- echo = false -------------------------------------------------------------------------------------------------------------------------- config <-System.file（“ extdata”，“ config.csv”，package =“ amplican”）config < - read.csv（config）knitr :: kable（head（config））## ---- configpath，echo = true，eval = false = false ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- file（“ extdata”，“ config.csv”，package =“ amplican”）## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------，eval = false ----------------------------------------------------＃＃示例配置文件＃配置<-系统。full path # results_folder <- tempdir() # # # run amplican # amplicanPipeline(config, fastq_folder, results_folder) # # # results of the analysis can be found at # message(results_folder) ## ---- echo=FALSE------------------------------------------------------------------------------------------------ barcodeFilters <- system.file("extdata", "results", "barcode_reads_filters.csv", package =“ amplican”）bar Codefilters <-Read.csv（bar codefilters）knitr :: kable（head（bar codefilters））## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------系统。“，” reads_filtered”，“ reads_in”，“ reads_del”，“ reads_edited”，“ reads_frameshifted”）] knitr :: kable（head（config_summary））＃-----------------------------------------------------------------------------------------＃路径到示例runparameters.txt run_params <-system.file（“ extdata”，“ rundparameters.txt”，package =“ amplican”）＃显示文件readlines（run_params）＃＃的内容＃＃----- echo = true，eval = false ----------------------------------------------------------------------------------------------------------------------------------------------------------＃＃示例对齐文件夹＃System.file（“ Extdata”，“结果”，“对齐”，package =“ Amplican”）## ---------------- echo=FALSE-------------------------------------------------------------- alignments <- system.file("extdata", "results", "alignments", "events_filtered_shifted_normalized.csv", package = "amplican") alignments <- read.csv(alignments) knitr::kable(head(alignments)) ## ---- echo=TRUE--------------------------------------------------------------- aln <- system.file("extdata", "results", "alignments", "AlignmentsExperimentSet.rds", package = "amplican") aln <- readRDS(aln) amplican::lookupAlignment(aln, ID = "ID_1") # will print most frequent alignment for ID_1