sc_gene_counting: sc_gene_counting

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

sc_gene_counting

Description

Generate gene counts matrix with UMI deduplication

Usage

sc_gene_counting(outdir, bc_anno, UMI_cor = 2, gene_fl = FALSE)

Arguments

outdir	output folder containing sc_demultiplex output
bc_anno	barcode annotation comma-separated-values, first column is cell id, second column is cell barcode sequence
UMI_cor	correct UMI sequencing error: 0 means no correction, 1 means simple correction and merge UMI with distance 1. 2 means merge on both UMI alignment position match.
gene_fl	whether to remove low abundance genes. A gene is considered to have low abundance if only one copy of one UMI is associated with it.

Value

no return

Examples

data_dir="celseq2_demo"
barcode_annotation_fn = system.file("extdata", "barcode_anno.csv",
package = "scPipe")
## Not run: 
# refer to the vignettes for the complete workflow
...
sc_gene_counting(data_dir, barcode_annotation_fn)
...

## End(Not run)

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