get_region_cov {brainflowprobes} | R Documentation

## Check or compute the region coverage from the datasets in brainflowprobes

### Description

This utility function checks the user-provided region data.frame coverage list (`COVERAGE`) or computes a new one using brainflowprobes_cov. This is used by four_panels and plot_coverage.

### Usage

    get_region_cov(
      REGION,
      COVERAGE = NULL,
      VERBOSE = TRUE,
      PD = brainflowprobes::pd
    )

### Arguments

`REGION` | Either a single hg19 genomic sequence including the chromosome, start, end, and optionally strand separated by colons (e.g., 'chr20:10199446-10288068:+'), or a string of sequences. Must be character. Chromosome must be proceeded by 'chr'.
`COVERAGE` | The output of brainflowprobes_cov for the input `REGION`. Defaults to `NULL` but it can be pre-computed and saved separately since this is the step that takes the longest to run. Also, this is the only step that depends on rtracklayer's functionality for reading BigWig files which does not run on Windows OS. So it could be run on a non-Windows machine, saved, and then shared with Windows users.
`VERBOSE` | A logical value indicating whether to print updates from the process of loading the data from the BigWig files.
`PD` | A list of data.frames with the `sumMapped` and `files` columns. Defaults to the data included in this package.

### Value

If `COVERAGE` is provided and all checks pass, then this function returns `COVERAGE`. Otherwise, it computes a new region coverage data.frame list using brainflowprobes_cov.

### Author(s)

Leonardo Collado-Torres

### Examples

    ## If all checks pass, then it returns the COVERAGE
    stopifnot(identical(
        get_region_cov(COVERAGE = four_panels_example_cov),
        four_panels_example_cov
    ))

[Package brainflowprobes version 1.4.1 Index]