QuickloadGenome-class {rtracklayer} | R Documentation

## Quickload Genome Access

### Description

A Quickload data source is a collection of tracks and sequences, separated by genome. This class, `QuickloadGenome` provides direct access to the data for one particular genome.

### Constructor

  `QuickloadGenome(quickload, genome, create = FALSE, seqinfo = seqinfo(genome), title = toString(genome))`: Constructs a new `QuickloadGenome` object, representing `genome` in the repository `quickload` (a URI string or a `Quickload` object).

  The `genome` argument can be an ID corresponding to a genome (potentially) in `quickload` or an installed `BSgenome` package. It can also be any instance of a class which has methods for `organism` and `releaseDate`. A good example is `BSgenome` or any other derivative of `GenomeDescription`. Those items are necessary for constructing the canonical Quickload genome string (G_Species_Month_Year).

  If `create` is `TRUE`, and the genome does not already exist, the genome will be created, using `seqinfo` for the sequence lengths and `title` for the display name of the genome in a UI. Creation only works if the repository is local and writeable. Reasonable defaults are used for `seqinfo` and `title` when the necessary methods are available (and they are for `BSgenome`).

### Accessor Methods

In the code snippets below, `x` and `object` represent a `Quickload` object.

  `seqinfo(x)`, `seqinfo(x) <- value`: Gets or sets the `Seqinfo` object indicating the lengths of the sequences in the genome. No circularity information or genome identifier is stored.

  `quickload(x)`: Get the Quickload object that contains this genome.

  `uri(x)`: Get the uri pointing to the genome directory in the Quickload repository

  `genome(x)`: Get the name of the genome, e.g. “H_sapiens_Feb_2009”.

  `releaseDate(x)`: Get the release portion of the genome name, e.g., “Feb_2009”.

  `organism(object)`: Get the organism portion of the genome name, e.g., “H sapiens”.

### Data Access

  `length(x)`: number of datasets

  `names(x), trackNames(x)`: names of the datasets

  `mcols(x)`: merged metadata on the datasets

  `track(x, name), x$name`: get the track called `name`

  `track(x, name, format = bestFileFormat(value), ...) <- value, x$name <- value`: store the track `value` under `name`. Note that track storing is only supported for local repositories, i.e., those with a `file://` URI scheme.

  Currently, supported `value` types include a `GenomicRanges`, `GRangesList`, or a file resource (copied to the repository). The file resource may be represented as a path, URL, `RTLFile` or `RsamtoolsFile`. If not a file name, `value` is written in `format`. For generic interval data, this means a BigWig file (if there is a numeric “score” column) or a BED file otherwise. An `RleList` (e.g., coverage) is output as BigWig. For `UCSCData` values, the format is chosen according to the type of track line. For `RsamtoolsFile` objects, the file and its index are copied.

  The arguments in `...` become attributes in the XML metadata. The “description” attribute is standard and is a blurb for describing the track in a UI. For the rest, the interpretation is up to the client. IGB supports an ever-growing list; please see its documentation.

  `referenceSequence(x)`: Get the reference sequence, as a `DNAStringSet`.

  `referenceSequence(x) <- value`: Set the reference sequence, as a `DNAStringSet`. It is written as a 2bit file. This only works on local repositories.

### Author(s)

Michael Lawrence

### Examples

    tests_dir <- system.file("tests", package = "rtracklayer")
    ql <- Quickload(file.path(tests_dir, "quickload"))
    qlg <- QuickloadGenome(ql, "T_species_Oct_2011")
    seqinfo(qlg)
    organism(qlg)
    releaseDate(qlg)
    names(qlg)
    mcols(qlg)
    if (.Platform$OS.type != "windows") { # temporary
    qlg$bedData
    }

    ## Not run:
    ## populating the test repository
    ql <- Quickload(file.path(tests_dir, "quickload"), create = TRUE)
    reference_seq <- import(file.path(tests_dir, "test.2bit"))
    names(reference_seq) <- "test"
    qlg <- QuickloadGenome(ql, "T_species_Oct_2011", create = TRUE,
                           seqinfo = seqinfo(reference_seq))
    referenceSequence(qlg) <- reference_seq
    test_bed <- import(file.path(tests_dir, "test.bed"))
    names(test_bed) <- "test"
    qlg$bedData <- test_bed
    test_bedGraph <- import(file.path(tests_dir, "test.bedGraph"))
    names(test_bedGraph) <- "test"
    start(test_bedGraph) <- seq(1, 90, 10)
    width(test_bedGraph) <- 10
    track(qlg, "bedGraphData", format = "bw") <- test_bedGraph

    ## End(Not run)

[Package rtracklayer version 1.42.2 Index]