runDropletQC: Perform comprehensive droplet QC

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

Perform comprehensive droplet QC

Description

A wrapper function to run several QC algorithms for determining empty droplets in single cell RNA-seq data

Usage

runDropletQC(
  inSCE,
  algorithms = c("QCMetrics", "emptyDrops", "barcodeRanks"),
  sample = NULL,
  useAssay = "counts",
  paramsList = NULL
)

Arguments

inSCE	A SingleCellExperiment object containing the full droplet count matrix
algorithms	Character vector. Specify which QC algorithms to run. Available options are "emptyDrops" and "barcodeRanks".
sample	Character vector. Indicates which sample each cell belongs to. Algorithms will be run on cells from each sample separately.
useAssay	A string specifying which assay contains the count matrix for droplets.
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")
## Not run: 
sce <- runDropletQC(sce)

## End(Not run)

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