Creates a table of QC metrics generated from QC algorithms via either kable or csv file.
sampleSummaryStats(inSCE, sample = NULL, useAssay = "counts", simple = TRUE)
| inSCE | Input SingleCellExperiment object with saved assay data and/or colData data. Required. |
|---|---|
| sample | Character vector. Indicates which sample each cell belongs to. |
| useAssay | A string specifying which assay in the SCE to use. Default 'counts'. |
| 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. |
A matrix/array object.
data(scExample, package = "singleCellTK") sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") sampleSummaryStats(sce, simple = TRUE)#> Total #> Number of Cells 195.00 #> Mean counts 3150.00 #> Median counts 2678.00 #> Mean features detected 181.59 #> Median features detected 183.00