## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----installation, eval=FALSE------------------------------------------------- # ## Install from Bioconductor # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("PoDCall") # # # ## Alternatively install PoDCall from GitHub # install.packages("devtools") # devtools::install_github("HansPetterBrodal/PoDCall") # # ## Install PoDCall from source file # install.packages("remotes") # remotes::install_local("path/to/PoDCall_x.y.z.tar.gz") # ## ----loading, eval=TRUE------------------------------------------------------- library(PoDCall) ## ---- eval=FALSE-------------------------------------------------------------- # ## Run PoDCall # thresholdTable <- podcallDdpcr(dataDirectory="path/to/data/") ## ----import-amplitude-data, echo=TRUE----------------------------------------- ## Path to example data files included in PoDCall path <- system.file("extdata", "Amplitudes/", package="PoDCall") ## Read in data files dataList <- importAmplitudeData(dataDirectory=path) str(dataList) ## ----import-sample-sheet, echo=TRUE------------------------------------------- ## Path to example files included in PoDCall path <- system.file("extdata", "Sample_names.csv", package="PoDCall") ## Select wells to get information for well_id <- c("A04", "B04", "D04") ## Read in sample sheet information for selected wells sampleSheet <- importSampleSheet(sampleSheet=path, well_id=well_id) print(sampleSheet) ## ----set-thresholds, eval=FALSE----------------------------------------------- # ## Path to example data files included in PoDCall # path <- system.file("extdata", "Amplitudes/", package="PoDCall") # # ## Read in data files # ampData <- importAmplitudeData(dataDirectory=path) # # ## Calculate thresholds, metrics, concentrations # thresholdTable <- podcallThresholds(plateData=ampData) # print(thresholdTable) ## ----channel-plot, echo=TRUE-------------------------------------------------- ## Read in data and threshold table path <- system.file("extdata", "Amplitudes/", package="PoDCall") ampData <- importAmplitudeData(dataDirectory=path) data("thrTable") thresholdTable <- thrTable ## Select channel and well to plot ch <- 1 # target channel well_id <- names(ampData)[1] # First well in list ## Plot title plotTitle <- paste0(well_id, ", Ch", ch) ## Create plot podcallChannelPlot(channelData=ampData[[well_id]][,ch], thr=thresholdTable[well_id, "thr_target"], channel=ch, plotId=plotTitle) ## ----scatter-plot, echo=TRUE-------------------------------------------------- ## Read in data and threshold table path <- system.file("extdata", "Amplitudes/", package="PoDCall") ampData <- importAmplitudeData(dataDirectory=path) thresholdTable <- thrTable ## Select channel and well to plot ch <- 1 # target channel well_id <- names(ampData)[1] # First well in list ## Plot title plotTitle <- paste0(well_id, ", Ch", ch) ## Create plot podcallScatterplot(channelData=ampData[[well_id]][,ch], thr=thresholdTable[well_id, "thr_target"], channel=ch, plotId=plotTitle) ## ----plot-histogram, echo=TRUE------------------------------------------------ ## Read in data and threshold table path <- system.file("extdata", "Amplitudes/", package="PoDCall") ampData <- importAmplitudeData(dataDirectory=path) thresholdTable <- thrTable ## Select channel and well to plot ch <- 1 # target channel well_id <- names(ampData)[1] # First well in list ## Plot title plotTitle <- paste0(well_id, ", Ch", ch) ## Create plot podcallHistogram(channelData=ampData[[well_id]][,ch], thr=thresholdTable[well_id, "thr_target"], channel=ch, plotId=plotTitle) ## ----comparison-plot, echo=TRUE----------------------------------------------- ## Read in data and threshold table path <- system.file("extdata", "Amplitudes/", package="PoDCall") ampData <- importAmplitudeData(dataDirectory=path) thresholdTable <- thrTable ## Channel to plot ch <- 1 ## Create comparison plot podcallMultiplot(plateData=ampData, thresholds=thresholdTable[names(ampData),], channel=ch) ## ----launch-shiny-app, eval=FALSE--------------------------------------------- # podcallShiny() ## ----example-data, eval=TRUE-------------------------------------------------- ## Path to files path <- system.file("extdata", "Amplitudes/", package="PoDCall") ## List files list.files(path) ## ----example-thresholds, echo=TRUE-------------------------------------------- ## The threshold table thrTable ## ----session-info, eval=TRUE-------------------------------------------------- sessionInfo()