counterUMI4C {UMI4Cats} | R Documentation

## UMI counting

### Description

Algorithm for counting and collapsing the number of UMIs supporting a specific ligation.

### Usage

    counterUMI4C(
      wk_dir,
      pos_viewpoint,
      res_enz,
      digested_genome,
      filter_bp = 1e+07
    )

### Arguments

`wk_dir` | Working directory where to save the outputs generated by the UMI-4c analysis.
`pos_viewpoint` | GRanges object containing the genomic position of the viewpoint.
`res_enz` | Character containing the restriction enzyme sequence.
`digested_genome` | Path for the digested genome file generated using the `digestGenome` function.
`filter_bp` | Integer indicating the bp upstream and downstream of the viewpoint to select for further analysis. Default=10e6.

### Details

For collapsing different molecules into the same UMI, takes into account the ligation position and the number of UMI sequence mismatches.

### Value

Creates a compressed tab-delimited file in `wk_dir/count` named "`basename(fastq) _counts.tsv.gz`", containing the coordinates for the viewpoint fragment, contact fragment and the number of UMIs detected in the ligation.

### Examples

    if (interactive()) {
    path <- downloadUMI4CexampleData(reduced = TRUE)

    hg19_dpnii <- digestGenome(
        cut_pos = 0,
        res_enz = "GATC",
        name_RE = "DpnII",
        sel_chr = "chr16", # digest only chr16 to make example faster
        ref_gen = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
        out_path = file.path(path, "digested_genome")
    )

    viewpoint <- GenomicRanges::GRanges("chr16:10972515-10972548")

    counterUMI4C(
        wk_dir = file.path(path, "CIITA"),
        pos_viewpoint = viewpoint,
        res_enz = "GATC",
        digested_genome = hg19_dpnii
    )

    }

[Package UMI4Cats version 1.4.0 Index]