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 0.99.31 Index]