## ----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()