sampleSummaryStats: Generate table of SCTK QC outputs.

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

Description

Creates a table of QC metrics generated from QC algorithms via either kable or csv file.

Usage

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

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.

Value

A matrix/array object.

Examples

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

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.