Stores and returns table of SCTK QC outputs to metadata.

Stores and returns table of QC metrics generated from QC algorithms within the metadata slot of the SingleCellExperiment object.

getSampleSummaryStatsTable(inSCE, statsName, ...)

setSampleSummaryStatsTable(inSCE, statsName, ...) <- value

# S4 method for SingleCellExperiment
getSampleSummaryStatsTable(inSCE, statsName, ...)

# S4 method for SingleCellExperiment
setSampleSummaryStatsTable(inSCE, statsName, ...) <- value

Arguments

inSCE

Input SingleCellExperiment object with saved assay data and/or colData data. Required.

statsName

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.

value

The summary table for QC statistics generated from SingleCellTK to be added to the SCE object.

Value

For getSampleSummaryStatsTable, A matrix/array object. Contains a summary table for QC statistics generated from SingleCellTK. For setSampleSummaryStatsTable<-, A SingleCellExperiment object where the summary table is updated in the metadata slot.

Examples

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