Get .html report of the output of the selected QC algorithm

A function to generate .html Rmarkdown report for the specified QC algorithm output

reportQCTool(
  inSCE,
  algorithm = c("BarcodeRankDrops", "EmptyDrops", "QCMetrics", "Scrublet", "ScDblFinder",
    "Cxds", "Bcds", "CxdsBcdsHybrid", "DoubletFinder", "DecontX", "SoupX"),
  output_file = NULL,
  output_dir = NULL
)

Arguments

inSCE: A SingleCellExperiment object containing the count matrix (full droplets or filtered matrix, depends on the selected QC algorithm) with the output from at least one of these functions: runQCMetrics, runScrublet, runScDblFinder, runCxds, runBcds, runCxdsBcdsHybrid, runDecontX, runBarcodeRankDrops, runEmptyDrops
algorithm: Character. Specifies which QC algorithm report to generate. Available options are "BarcodeRankDrops", "EmptyDrops", "QCMetrics", "Scrublet", "ScDblFinder", "Cxds", "Bcds", "CxdsBcdsHybrid", "DoubletFinder", "DecontX" and "SoupX".
output_file: name of the generated file. If NULL/default then the output file name will be based on the name of the selected QC algorithm name .
output_dir: name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory

Value

.html file

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
if (FALSE) {
sce <- runDecontX(sce)
sce <- runQuickUMAP(sce)
reportQCTool(inSCE = sce, algorithm = "DecontX")
}