get_coverage {ODER} | R Documentation

## Obtain the mean coverage across multiple BigWig files

### Description

`get_coverage` returns the mean coverage of the BigWig files passed in. Internally, this operates through `derfinder::loadCoverage`.

### Usage

    get_coverage(
      bw_paths,
      auc_raw,
      auc_target,
      chrs = "",
      genome = "hg38",
      bw_chr = "chr"
    )

### Arguments

`bw_paths` | path(s) to bigwig file(s) with the RNA-seq data that you want the #' coverage of.
`auc_raw` | vector containing AUCs(Area Under Coverage) matching the order of bigwig path(s).
`auc_target` | total AUC to normalise all samples to e.g. 40e6 * 100 would be the estimated total auc for sample sequenced to 40 million reads of 100bp in length.
`chrs` | chromosomes to obtain mean coverage for, default is "" giving every chromosome. Can take UCSC format(chrs = "chr1") or just the chromosome i.e. chrs = c(1,X)
`genome` | the UCSC genome you want to use, the default is hg38.
`bw_chr` | specifies whether the bigwig files has the chromosomes labelled with a "chr" preceding the chromosome i.e. "chr1" vs "1". Can be either "chr" or "nochr" with "chr" being the default.

### Value

a list of Rles detailing the mean coverage per chromosome passed in.

### Examples

    rec_url <- recount::download_study(
        project = "SRP012682",
        type = "samples",
        download = FALSE
    )
    bw_path <- file_cache(rec_url[1])
    # As of rtracklayer 1.25.16, BigWig is not supported on Windows.
    if (!xfun::is_windows()) {
        eg_coverage <- get_coverage(
            bw_paths = bw_path,
            auc_raw = 11872688252,
            auc_target = 40e6 * 100,
            chrs = c("chr21", "chr22")
        )
        eg_coverage
    }

[Package ODER version 1.0.0 Index]