Description Usage Arguments Value Examples
View source: R/dropletUtils_barcodeRank.R
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.
1 2 3 4 5 6 7 8 | 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.
1 2 3 4 5 6 7 8 9 10 | # 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)
|
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