Identify empty droplets

This function is used to identify a suitable nuclear fraction cut-off point to guide the identification of empty droplets. To do this it calculates the kernel density estimate of the input nuclear fraction scores and identifies the trough after the first peak, which is assumed to represent the population of empty droplets.

identify_empty_drops(
  nf_umi,
  nf_rescue = 0.05,
  umi_rescue = 1000,
  include_plot = FALSE,
  plot_name = NULL,
  plot_path = NULL,
  plot_width = 18,
  plot_height = 13,
  pdf_png = "png"
)

Arguments

nf_umi	data frame, containing two columns; the nuclear fraction estimates in the first column and the total UMI count for each barcode in the second column
nf_rescue	numeric, a rescue parameter defining a minimum nuclear fraction score between zero and one. This is used in combination with umi_rescue to identify cells that were misidentified as empty droplets
umi_rescue	integer, a rescue parameter defining a minimum UMI count. This is used in combination with nf_rescue to identify cells that were misidentified as empty droplets
include_plot	logical, whether or not to produce a plot illustrating how the nuclear fraction threshold was identified and which barcodes have been called as empty droplets. In the plot of nuclear fraction vs log10(UMI counts), empty droplets are expected to occupy the lower left corner of the plot.
plot_name	character, if provided a plot will be saved with the provided name
plot_path	character, if provided a plot will be saved to the provided path
plot_width	numeric, plot width in cm
plot_height	numeric, plot height in cm
pdf_png	character, either "png" or "pdf"

Value

data frame, the original data frame is returned plus an additional column identifying each barcode as a "cell" or "empty_droplet"

Examples

data("qc_examples")
gbm <- qc_examples[qc_examples$sample=="GBM",]
gbm.ed <- gbm[,c("nuclear_fraction_droplet_qc","umi_count")]
gbm.ed <- identify_empty_drops(nf_umi = gbm.ed)
head(gbm.ed)
#>                    nuclear_fraction_droplet_qc umi_count cell_status
#> AAACCCAAGGCGATAC-1                   0.1947243      2226        cell
#> AAACCCAAGGCTGTAG-1                   0.2766798      1063        cell
#> AAACCCACAAGTCCCG-1                   0.1843824     17883        cell
#> AAACCCACAGATGCGA-1                   0.2919902      8172        cell
#> AAACCCACAGGTGAGT-1                   0.3295617      9057        cell
#> AAACCCAGTCTTGCGG-1                   0.3795893      5612        cell
table(gbm.ed$cell_status)
#> 
#>          cell empty_droplet 
#>          5296           220