reportCellQC: Get runCellQC .html report

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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,
  useReducedDim = NULL
)

Arguments

inSCE	A SingleCellExperiment object containing the filtered count matrix with the output from runCellQC function
output_file	Character. The 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	Character. The 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	Character. The description of the data set and experiment design. It would be shown at the top of QC HTML report. Default is NULL.
useReducedDim	Character. The name of the saved dimension reduction slot including cells from all samples in thenSingleCellExperiment object, 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)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.