runBarcodeRankDrops {singleCellTK} | R Documentation |
Run barcodeRanks on a count matrix provided in a SingleCellExperiment object. Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.
runBarcodeRankDrops( inSCE, sample = NULL, useAssay = "counts", lower = 100, fitBounds = NULL, df = 20 )
inSCE |
A SingleCellExperiment object. Must contain a raw counts matrix before empty droplets have been removed. |
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 |
useAssay |
A string specifying which assay in the SCE to use. |
lower |
See emptyDrops for more information. Default |
fitBounds |
See emptyDrops for more information. Default |
df |
See emptyDrops for more information. Default |
A SingleCellExperiment object with the barcodeRanks output table appended to the colData slot. The columns include dropletUtils_BarcodeRank_Knee and dropletUtils_BarcodeRank_Knee Please refer to the documentation of barcodeRanks 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 tutoriol on how to # run the function. The results should not be # used for drawing scientific conclusions. data(scExample, package = "singleCellTK") sce <- runBarcodeRankDrops(inSCE = sce)