RLRanges-class {RLSeq} | R Documentation

## Construct RLRanges Dataset

### Description

`RLRanges` is a subclass of `GRanges`, which stores R-loop peaks and metadata about the R-loop-mapping experiment, along with results from the analyses in RLSeq.

### Usage

    RLRanges(
      peaks = GenomicRanges::GRanges(),
      coverage = character(1),
      genome = character(1),
      mode = character(1),
      label = character(1),
      sampleName = "User-selected sample",
      qcol = NULL
    )

### Arguments

`peaks` | Path/URL to peak file or a GRanges object. This file should be in "broadPeak" format if possible. If not, then `qcol` should be specified.
`coverage` | Path/URL to the coresponding coverage file (in "bigWig" format). If not supplied, correlation tests will be skipped.
`genome` | UCSC genome ID. Acceptable types are listed in auxdata (`available_genomes` entry).
`mode` | Type of R-loop mapping from which peaks and coverage were derived. Acceptable types are listed in auxdata (`available_modes` entry). Can be unspecified.
`label` | "POS" (positive R-loop-mapping sample; e.g., DRIP-Seq S9.6 -RNH1) or "NEG" (negative control sample; e.g., DRIP-Seq S9.6 +RNH1 or Input). Can be unspecified.
`sampleName` | A unique name for identifying this sample. Can be unspecified.
`qcol` | The name of the metadata column which contains the score or significance of each peak. For broadPeak (preferred), this is the qvalue (column 11 after accounting for extra columns created during peakset building). If not specified, the last column will be chosen by default. NOTE: if supplying narrowPeak form peaks, the last column will NOT be appropriate and QCol should be specified as `11`. If FALSE or if no metadata columns exist, it will be left blank and some operations in `report()` will not fully run.

### Value

An object of class `RLRanges`. These objects are an extension of `GRanges` with the addition of sample metadata entries and RLResults.

### Examples

    # Example dataset
    rlbase <- "https://rlbase-data.s3.amazonaws.com"
    cvg <- file.path(rlbase, "coverage", "SRX7671349_hg38.bw")
    pks <- system.file("extdata", "SRX7671349_hg38.broadPeak", package="RLSeq")

    # Get RLRanges object
    rlr <- RLRanges(pks,
        coverage = cvg, genome = "hg38", label = "NEG",
        mode = "RDIP", sampleName = "RDIP-Seq +RNH1", qcol = 9
    )

[Package RLSeq version 1.0.0 Index]