reportQCTool {singleCellTK} | R Documentation

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

### Description

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

### Usage

    reportQCTool(
      inSCE,
      algorithm = c("BarcodeRankDrops", "EmptyDrops", "QCMetrics", "Scrublet",
        "ScDblFinder", "Cxds", "Bcds", "CxdsBcdsHybrid", "DoubletFinder", "DecontX"),
      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" and "DecontX".
`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'")
    ## Not run:
    sce <- runDecontX(sce)
    sce <- getUMAP(sce)
    reportQCTool(inSCE = sce, algorithm = "DecontX")

    ## End(Not run)

[Package singleCellTK version 2.2.0 Index]