get_coverage {ODER} | R Documentation |
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 }