get_coverage: Obtain the mean coverage across multiple BigWig files
In eolagbaju/ODER: Optimising the Definition of Expressed Regions

Description Usage Arguments Value Examples

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

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

`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.

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

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
}