% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/sampleSummaryStats.R
 \name{sampleSummaryStats}
 \alias{sampleSummaryStats}

 \title{Generate table of SCTK QC outputs.}

 \usage{

 sampleSummaryStats(
   inSCE,
   sample = NULL,
   useAssay = "counts",
   simple = TRUE,
   statsName = "qc_table"
 )

 }
 \arguments{
 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved

 \link{assay} data and/or \link{colData} data. Required.}

 
 \item{sample}{Character vector. Indicates which sample each cell belongs to.}
 
 \item{useAssay}{A string specifying which assay in the SCE to use. Default
 'counts'.}
 
 \item{simple}{Boolean. Indicates whether to generate a table of only
 basic QC stats (ex. library size), or to generate a summary table of all
 QC stats stored in the inSCE.}

 
 \item{statsName}{Character. The name of the slot that will store the
 QC stat table. Default "qc_table".}

 }

 \value{

 A SingleCellExperiment object with a summary table for QC statistics

 in the `sample_summary` slot of metadata.

 }

 \description{

 Creates a table of QC metrics generated from

  QC algorithms, which is stored within the metadata slot of the
  input SingleCellExperiment object.

 }
 \examples{
 data(scExample, package = "singleCellTK")

 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

 sce <- sampleSummaryStats(sce, simple = TRUE)

 getSampleSummaryStatsTable(sce, statsName = "qc_table")

 }