sampleSummaryStats: Generate table of SCTK QC outputs.

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

Generate table of SCTK QC outputs.

Description

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

Usage

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")

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.