Run emptyDrops on the count matrix in the provided SingleCellExperiment object. Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.
runEmptyDrops( inSCE, sample = NULL, useAssay = "counts", lower = 100, niters = 10000, testAmbient = FALSE, ignore = NULL, alpha = NULL, retain = NULL, barcodeArgs = list(), BPPARAM = BiocParallel::SerialParam() )
inSCE | Input SingleCellExperiment object. Must contain a raw counts matrix before empty droplets have been removed. |
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sample | Character vector. Indicates which sample each cell belongs to. emptyDrops will be run on cells from each sample separately. If NULL, then all cells will be processed together. Default NULL. |
useAssay | A string specifying which assay in the SCE to use. |
lower | See emptyDrops for more information. |
niters | See emptyDrops for more information. |
testAmbient | See emptyDrops for more information. |
ignore | See emptyDrops for more information. |
alpha | See emptyDrops for more information. |
retain | See emptyDrops for more information. |
barcodeArgs | See emptyDrops for more information. |
BPPARAM | See emptyDrops for more information. |
A SingleCellExperiment object with the emptyDrops output table appended to the colData slot. The columns include emptyDrops_total, emptyDrops_logprob, emptyDrops_pvalue, emptyDrops_limited, emptyDrops_fdr. Please refer to the documentation of emptyDrops for details.
# The following unfiltered PBMC_1k_v3 data were downloaded from # https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0 # /pbmc_1k_v3 # Only the top 10 cells with most counts and the last 10 cells with non-zero # counts are included in this example. # This example only serves as an proof of concept and a tutorial on how to # run the function. The results should not be # used for drawing scientific conclusions. data(scExample, package = "singleCellTK") sce <- runEmptyDrops(inSCE = sce)#>