QuickloadGenome-class: Quickload Genome Access

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

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)

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.