sc_atac_cell_calling: identifying true vs empty cells

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

identifying true vs empty cells

Description

the methods to call true cells are of various ways. implement (i.e. filtering from scATAC-Pro as default

Usage

sc_atac_cell_calling(
  mat,
  cell_calling = "filter",
  output_folder,
  genome_size = NULL,
  cell_qc_metrics_file = NULL,
  lower = NULL,
  min_uniq_frags = 3000,
  max_uniq_frags = 50000,
  min_frac_peak = 0.3,
  min_frac_tss = 0,
  min_frac_enhancer = 0,
  min_frac_promoter = 0.1,
  max_frac_mito = 0.15
)

Arguments

mat	the feature by cell matrix.
cell_calling	the cell calling approach, possible options were "emptydrops" , "cellranger" and "filter". But we opten to using "filter" as it was most robust. "emptydrops" is still an opition for data with large umber of cells.
output_folder	output directory for the cell called matrix.
genome_size	genome size for the data in feature by cell matrix.
cell_qc_metrics_file	quality per barcode file for the barcodes in the matrix if using the cellranger or filter options.
lower	the lower threshold for the data if using the emptydrops function for cell calling.
min_uniq_frags	The minimum number of required unique fragments required for a cell (used for filter cell calling)
max_uniq_frags	The maximum number of required unique fragments required for a cell (used for filter cell calling)
min_frac_peak	The minimum proportion of fragments in a cell to overlap with a peak (used for filter cell calling)
min_frac_tss	The minimum proportion of fragments in a cell to overlap with a tss (used for filter cell calling)
min_frac_enhancer	The minimum proportion of fragments in a cell to overlap with a enhancer sequence (used for filter cell calling)
min_frac_promoter	The minimum proportion of fragments in a cell to overlap with a promoter sequence (used for filter cell calling)
max_frac_mito	The maximum proportion of fragments in a cell that are mitochondrial (used for filter cell calling)

Examples

## Not run: 
sc_atac_cell_calling <- function(mat,
 cell_calling,
 output_folder,
 genome_size    = NULL,
 cell_qc_metrics_file = NULL,
 lower          = NULL)

## End(Not run)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.