Generate table of SCTK QC outputs.

Creates a table of QC metrics generated from QC algorithms, which is stored within the metadata slot of the input SingleCellExperiment object.

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

Arguments

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.

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.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- sampleSummaryStats(sce, simple = TRUE)
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