sc_gene_counting {scPipe} | R Documentation

## 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)

[Package scPipe version 1.4.1 Index]