get_ers {ODER} | R Documentation

## Define sets of ERs

### Description

`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.

### Usage

    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"
    )

### Arguments

`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.

### Value

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.

### Functions

- `get_strand_ers`: Method for getting ers from stranded BigWig files

### Examples

    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
    }

[Package ODER version 1.0.0 Index]