find_nonambient_barcodes: Call barcodes as being sufficiently distinct from the ambient...

In zh542370159/dropSplit: Automatically identify cell-containing and empty droplets for droplet-based scRNAseq data using dropSplit

Call barcodes as being sufficiently distinct from the ambient profile

Description

Call barcodes as being sufficiently distinct from the ambient profile

Usage

find_nonambient_barcodes(
  matrix,
  orig_cell_bcs,
  n_partitions = 90000,
  n_candidate_barcodes = 20000,
  min_umis_nonambient = 500,
  min_umi_frac_of_median = 0.01,
  max_adj_pvalue = 0.01
)

Arguments

matrix	Full expression matrix.
orig_cell_bcs	Strings of initially-called cell barcodes.
n_partitions	Number of partitions (max number of barcodes to consider for ambient estimation). Default is 90000.
n_candidate_barcodes	Number of additional barcodes to consider after the initial cell calling. Default is 20000.
min_umis_nonambient	Minimum number of UMIS per barcode to consider after the initial cell calling. Default is 500.
min_umi_frac_of_median	Minimum ratio of UMIs to the median (initial cell call UMI) to consider after the initial cell calling. Default is 0.01.
max_adj_pvalue	Minimum ratio of UMIs to the median (initial cell call UMI) to consider after the initial cell calling. Default is 0.01.

Value

A data.frame.

zh542370159/dropSplit documentation built on June 19, 2022, 2:49 p.m.