get_ers: Define sets of ERs
In eolagbaju/ODER: Optimising the Definition of Expressed Regions

Description Usage Arguments Value Functions Examples

get_ers defines expressed regions across an inputted range of mean coverage cut-offs (MCCs) and max region gaps (MRGs) from the coverage.

get_strand_ers defines ERs across an inputted range of mean coverage cut-offs (MCCs) and max region gaps (MRGs) from the coverage.

get_ers(coverage, mccs, mrgs)

get_strand_ers(
  bw_pos,
  bw_neg,
  auc_raw_pos,
  auc_raw_neg,
  auc_target,
  chrs,
  mccs,
  mrgs,
  bw_chr = "chr"
)

`coverage`	the coverage of the bigwig files passed into `get_coverage`.
`mccs`	mean coverage cut-offs to apply.
`mrgs`	max region gaps to apply.
`bw_pos`	positive strand bigwig file
`bw_neg`	negative strand bigwig file
`auc_raw_pos`	vector containing AUCs(Area Under Coverage) matching the order of the positive bigwig paths.
`auc_raw_neg`	vector containing AUCs(Area Under Coverage) matching the order of the negative bigwig paths.
`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)
`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.

list containing sets of ERs, each generated using a particular combination of MCC and MRG.

list containing sets of stranded ERs, each generated using a particular combination of MCC and MRG.

get_strand_ers: Method for getting ers from stranded BigWig files

data(gtex_SRP012682_SRX222703_lung_coverage_1, package = "ODER")

eg_ers <- get_ers(
    coverage = gtex_SRP012682_SRX222703_lung_coverage_1,
    mccs = c(5, 10),
    mrgs = c(10, 20)
)

eg_ers
library("magrittr")
gtex_metadata <- recount::all_metadata("gtex")
gtex_metadata <- gtex_metadata %>%
    as.data.frame() %>%
    dplyr::filter(project == "SRP012682")

rec_url <- recount::download_study(
    project = "SRP012682",
    type = "samples",
    download = FALSE
)
# file_cache is an internal function to download a bigwig file from a link
# if the file has been downloaded recently, it will be retrieved from a cache
bw_plus <- file_cache(rec_url[58])
bw_minus <- file_cache(rec_url[84])

# As of rtracklayer 1.25.16, BigWig is not supported on Windows.
if (!xfun::is_windows()) {
    stranded_ers <- get_strand_ers(
        bw_pos = bw_plus, bw_neg = bw_minus,
        auc_raw_pos = gtex_metadata[["auc"]][58],
        auc_raw_neg = gtex_metadata[["auc"]][84], auc_target = 40e6 * 100,
        chrs = "chr21", mccs = c(5, 10), mrgs = c(10, 20)
    )
    stranded_ers
}