A wrapper function to run several QC algorithms for determining empty droplets in single cell RNA-seq data
runDropletQC( inSCE, algorithms = c("QCMetrics", "emptyDrops", "barcodeRanks"), sample = NULL, useAssay = "counts", paramsList = NULL )
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. |
SingleCellExperiment object containing the outputs of the
specified algorithms in the colData
of inSCE
.