## ----include=FALSE--------------------------------------------------------- library(BiocStyle) ## ----load, message=FALSE--------------------------------------------------- library(Rqc) ## ----file_loc-------------------------------------------------------------- folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147") ## ---- rqc, eval=FALSE------------------------------------------------------ # rqc(path = folder, pattern = ".fastq.gz") ## ----example, echo=FALSE, message=FALSE------------------------------------ fastqDir <- system.file(package="ShortRead", "extdata/E-MTAB-1147") files <- list.files(fastqDir, "fastq.gz", full.names=TRUE) qa <- rqcQA(files, workers=1) ## -------------------------------------------------------------------------- knitr::kable(perFileInformation(qa)) ## ----read-mean-dist-------------------------------------------------------- rqcReadQualityBoxPlot(qa) ## ----average-quality-plot-------------------------------------------------- rqcReadQualityPlot(qa) ## ----cycle-average-quality-plot-------------------------------------------- rqcCycleAverageQualityPlot(qa) ## ----readfrequency--------------------------------------------------------- rqcReadFrequencyPlot(qa) ## ----heatmap-reads--------------------------------------------------------- rqcFileHeatmap(qa[[1]]) ## ----read-width-plot------------------------------------------------------- rqcReadWidthPlot(qa) ## ----cycle-gc-plot--------------------------------------------------------- rqcCycleGCPlot(qa) ## ----cycle-quality-plots--------------------------------------------------- rqcCycleQualityPlot(qa) ## ----biplot---------------------------------------------------------------- rqcCycleAverageQualityPcaPlot(qa) ## ----cycle-quality-boxplots------------------------------------------------ rqcCycleQualityBoxPlot(qa) ## ----cycle-basecall-plots-------------------------------------------------- rqcCycleBaseCallsPlot(qa) ## ----cycle-basecall-lineplots---------------------------------------------- rqcCycleBaseCallsLinePlot(qa) ## ----input----------------------------------------------------------------- fastqDir <- system.file(package="ShortRead", "extdata/E-MTAB-1147") files <- list.files(fastqDir, "fastq.gz", full.names=TRUE) ## ----rqcQA----------------------------------------------------------------- qa <- rqcQA(files, workers=1) ## ----report, eval=FALSE---------------------------------------------------- # reportFile <- rqcReport(qa) # browseURL(reportFile) ## ----calc------------------------------------------------------------------ df <- rqcCycleAverageQualityCalc(qa) cycle <- as.numeric(levels(df$cycle))[df$cycle] plot(cycle, df$quality, col = df$filename, xlab='Cycle', ylab='Quality Score') ## ----subset---------------------------------------------------------------- sublist <- qa[1] rqcCycleQualityPlot(sublist) ## ----default-report-path, eval=FALSE--------------------------------------- # system.file(package = "Rqc", "templates", "rqc_report.Rmd") ## ----rqc-report-custom-template, eval=FALSE-------------------------------- # rqcReport(qa, templateFile = "custom_report.Rmd") ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()