runCellQC: Perform comprehensive single cell QC

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

Description

A wrapper function to run several QC algorithms on a SingleCellExperiment object containing cells after empty droplets have been removed.

Usage

runCellQC(
  inSCE,
  algorithms = c("QCMetrics", "doubletCells", "cxds", "bcds", "cxds_bcds_hybrid",
    "scrublet", "doubletFinder", "decontX"),
  sample = NULL,
  collectionName = NULL,
  geneSetList = NULL,
  geneSetListLocation = "rownames",
  geneSetCollection = NULL,
  useAssay = "counts",
  seed = 12345,
  paramsList = NULL
)

Arguments

inSCE	A SingleCellExperiment object.
algorithms	Character vector. Specify which QC algorithms to run. Available options are "QCMetrics", "scrublet", "doubletCells", "cxds", "bcds", "cxds_bcds_hybrid", and "decontX".
sample	Character vector. Indicates which sample each cell belongs to. Algorithms will be run on cells from each sample separately.
collectionName	Character. Name of a GeneSetCollection obtained by using one of the importGeneSet* functions. Default NULL.
geneSetList	See runPerCellQC. Default NULL.
geneSetListLocation	See runPerCellQC. Default NULL.
geneSetCollection	See runPerCellQC. Default NULL.
useAssay	A string specifying which assay contains the count matrix for cells.
seed	Seed for the random number generator. Default 12345.
paramsList	A list containing parameters for QC functions. Default NULL.

Value

SingleCellExperiment object containing the outputs of the specified algorithms in the colData of inSCE.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
## Not run: 
sce <- runCellQC(sce)

## End(Not run)

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