count_coverage {ChromSCape} | R Documentation

## Create a smoothed and normalized coverage track from a BAM file and given a bin GenomicRanges object (same as deepTools bamCoverage)

### Description

Normalization is CPM, smoothing is done by averaging on n_smoothBin regions left and right of any given region.

### Usage

    count_coverage(
      filename,
      format = "BAM",
      bins,
      canonical_chr,
      n_smoothBin = 5,
      ref = "hg38",
      read_size = 101
    )

### Arguments

`filename` | Path towards the BAM to create coverage from
`format` | File format, either "BAM" or "BED"
`bins` | A GenomicRanges object of binned genome
`canonical_chr` | GenomicRanges of the chromosomes to read the BAM file.
`n_smoothBin` | Number of bins left and right to smooth the signal.
`ref` | Genomic reference
`read_size` | Length of the reads

### Value

A binned GenomicRanges that can be readily exported into bigwig file.

[Package ChromSCape version 1.2.62 Index]