getSampleSummaryStatsTable: Stores and returns table of SCTK QC outputs to metadata.

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Stores and returns table of SCTK QC outputs to metadata.

Description

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

Usage

getSampleSummaryStatsTable(inSCE, statsName, ...)

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

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

## S4 replacement method for signature '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")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.