reportCellQC {singleCellTK} | R Documentation

## Get runCellQC .html report

### Description

A function to generate .html Rmarkdown report containing the visualizations of the runCellQC function output

### Usage

    reportCellQC(
      inSCE,
      output_file = NULL,
      output_dir = NULL,
      subTitle = NULL,
      studyDesign = NULL
    )

### Arguments

`inSCE` | A SingleCellExperiment object containing the filtered count matrix with the output from runCellQC function
`output_file` | name of the generated file. If NULL/default then the output file name will be based on the name of the Rmarkdown template.
`output_dir` | name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory
`subTitle` | subtitle of the QC HTML report. Default is NULL.
`studyDesign` | description of the data set and experiment design. It would be shown at the top of QC HTML report. Default is NULL.

### Value

.html file

### Examples

    data(scExample, package = "singleCellTK")
    sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
    ## Not run:
    sce <- runCellQC(sce)
    reportCellQC(inSCE = sce)

    ## End(Not run)

[Package singleCellTK version 2.0.0 Index]