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
)
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
Character. Specifies which QC algorithm report to generate. Available options are "BarcodeRankDrops", "EmptyDrops", "QCMetrics", "Scrublet", "ScDblFinder", "Cxds", "Bcds", "CxdsBcdsHybrid", "DoubletFinder", "DecontX" and "SoupX".
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 .
name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory
.html file
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
if (FALSE) {
sce <- runDecontX(sce)
sce <- getUMAP(sce)
reportQCTool(inSCE = sce, algorithm = "DecontX")
}