Get filter to remove ambient RNA barcodes based on the combination of multiple methods:

Source: R/filter_ambient_barcode.R

inflection - all barcodes below the inflection point in the UMI rank vs total UMI plot are called ambient knee - all barcodes below the knee in the UMI rank vs total UMI plot are called ambient cellranger (v2) - all barcodes below 10 empty_drops - uses the algorithm from DropletUtils::emptyDrops to compare each barcode to the profile of barcodes below

filter_ambient_barcode(
  sce,
  n_cells,
  fdr = 0.01,
  lower_umi_limit = 100,
  n_iters = 10000
)

Arguments

sce

SingleCellExperiment object
n_cells

number of input cells (used in cellranger cutoff computation)
fdr

FDR threshold for keeping a cell for emptyDrops
lower_umi_limit

number of total UMIs below which a barcode is assumed to contain ambient RNA, used in emptyDrops method only

Value

List for each method in containing filter for method and attributes with details specific to each method.

Examples

NULL
#> NULL