R/allGenerics.R
, R/sampleSummaryStats.R
getSampleSummaryStatsTable.Rd
Stores and returns table of QC metrics generated from QC algorithms within the metadata slot of the SingleCellExperiment object.
getSampleSummaryStatsTable(inSCE, statsName, ...)
# S4 method for SingleCellExperiment
getSampleSummaryStatsTable(inSCE, statsName, ...)
Input SingleCellExperiment object with saved assay data and/or colData data. Required.
A character
value indicating the slot
that stores the stats table within the metadata of the
SingleCellExperiment object. Required.
Other arguments passed to the function.
A matrix/array object. Contains a summary table for QC statistics generated from SingleCellTK.
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- sampleSummaryStats(sce, simple = TRUE, statsName = "qc_table")
getSampleSummaryStatsTable(sce, statsName = "qc_table")
#> All Samples
#> Number of Cells 195.00
#> Mean counts 3150.00
#> Median counts 2678.00
#> Mean features detected 181.59
#> Median features detected 183.00