sc_gene_counting {scPipe} | R Documentation |
Generate gene counts matrix with UMI deduplication
sc_gene_counting(outdir, bc_anno, UMI_cor = 2, gene_fl = FALSE)
outdir |
output folder containing |
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. |
no return
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)