TrackHubGenome-class {rtracklayer} | R Documentation

## TrackHub Genome Access

### Description

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

### Constructor

  `TrackHubGenome(trackhub, genome, create = FALSE`: Constructs a new `TrackHubGenome` object, representing `genome` in the repository `trackhub` (a URI string or a `TrackHub` object).

  The `genome` argument can be an ID corresponding to a genome (potentially) in `trackhub` or an installed `BSgenome` package.

  If `create` is `TRUE`, and the trackDb file does not already exist, it will be created. Creation only works if the repository is local and writeable.

### Accessor Methods

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

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

  `genome(x)`: Get the name of the genome, e.g. “hg19”.

  `length(x)`: number of tracks

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

  `getTracks(x)`: Get the `List` of `Track` from the tracks

  `trackhub(x)`: Get the TrackHub object that contains this genome.

  `organism(x)`: Get the organism name for this genome, e.g., “H sapiens”.

  `trackField(x, name, field)`: Get the `value` of `field` for `name` track.

  `trackField(x, name, field) <- value`: Store the `field` and `value` for `name` track.

  `writeTrackHub(x)`: Write tracks from memory representation to the trackDb file.

### Data Access

  `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, `BiocFile` 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.

  `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")
    th <- TrackHub(file.path(tests_dir, "trackhub"))
    thg <- TrackHubGenome(th, "hg19")
    length(thg)
    organism(thg)
    names(thg)

    ## Not run:
    th <- TrackHub(file.path(tests_dir, "trackhub"), create = TRUE)
    genomesFile(th) <- "genomes.txt"
    genomeInfo(th) <- Genome(genome = "hg38", trackDb = "hg38/trackDb.txt")
    genomeField(th, "hg38", "twoBitPath") <- "hg38/seq.2bit"
    writeTrackHub(th)
    thg <- TrackHubGenome(th, "hg38", create = TRUE)
    seq <- import(file.path(tests_dir, "test.2bit"))
    referenceSequence(thg) <- seq
    track(thg, "PeaksData") <- paste0(tests_dir, "/test.bigWig")
    trackField(thg, "wgEncodeUWDukeDnaseGM12878FdrPeaks", "bigDataUrl") <- "hg38/wgEncodeCshlShortRnaSeq.bigWig"
    trackField(thg, "wgEncodeUWDukeDnaseGM12878FdrPeaks", "color") <- "8,104,172"
    writeTrackHub(thg)

    ## End(Not run)

[Package rtracklayer version 1.52.1 Index]