## ---- echo=FALSE-------------------------------------------------------------- config <- system.file("extdata", "config.csv", package = "amplican") config <- read.csv(config) knitr::kable(head(config)) ## ----configPath, echo=TRUE, eval=FALSE---------------------------------------- # system.file("extdata", "config.csv", package = "amplican") ## ----amplicanPipeline, echo=TRUE, eval=FALSE---------------------------------- # # path to example config file # config <- system.file("extdata", "config.csv", package = "amplican") # # path to example fastq files # fastq_folder <- system.file("extdata", package = "amplican") # # output folder, a 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") barcodeFilters <- read.csv(barcodeFilters) knitr::kable(head(barcodeFilters)) ## ---- echo=FALSE-------------------------------------------------------------- config_summary <- system.file("extdata", "results", "config_summary.csv", package = "amplican") config_summary <- read.csv(config_summary) config_summary <- config_summary[, c("ID", "Barcode", "Reads", "Reads_Filtered", "Reads_In", "Reads_Del", "Reads_Edited", "Reads_Frameshifted")] knitr::kable(head(config_summary)) ## ---- echo=TRUE--------------------------------------------------------------- # path to example RunParameters.txt run_params <- system.file("extdata", "results", "RunParameters.txt", package = "amplican") # show contents of the file readLines(run_params) ## ---- echo=TRUE, eval=FALSE--------------------------------------------------- # # path to the example alignments folder # system.file("extdata", "results", "alignments", 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