QuickloadGenome-class(rtracklayer)
QuickloadGenome-class()所属R语言包：rtracklayer
Quickload Genome Access
quickload基因组访问
译者：生物统计家园网 机器人LoveR
描述----------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.
一个Quickload数据源收集的曲目和序列，通过基因分离。这个类，QuickloadGenome提供一个特定的基因组数据的直接访问。
构造----------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).
QuickloadGenome(quickload, genome, create = FALSE, seqinfo = seqinfo(genome), title = toString(genome))：构造一个新的QuickloadGenome对象，代表genome在库quickload（一个URI字符串或一个Quickload对象）。
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).
genome参数可以是一个ID对应的基因组在quickload（潜在的）或安装BSgenome包。它也可以是任何一个具有organism和releaseDate方法的类的实例。一个很好的例子是BSgenome或任何其他衍生GenomeDescription。这些项目建设规范Quickload基因组字符串（G_Species_Month_Year）所必需的。
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).
如果create是TRUE和基因组已经不存在，将创建的基因组，使用seqinfo序列的长度和title的基因组中的显示名称在UI。创建仅适用于如果库是局部的和可写的。合理的默认值是用于seqinfo和title时必要的方法（和他们BSgenome）。
存取方法----------Accessor Methods----------
In the code snippets below, x represents a Quickload object.
在下面的代码片段，xQuickload对象。
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.
seqinfo(x)，seqinfo(x) <- value：获取或设置Seqinfo对象，说明在基因组序列的长度。不圆的信息或基因组标识符存储。
quickload(x): Get the Quickload object that contains this genome.
quickload(x)：获取的Quickload的对象，它包含此基因。
uri(x): Get the uri pointing to the genome directory in the Quickload repository
uri(x)：获取URI指向的基因组在Quickload库目录
genome(x): Get the name of the genome, e.g. “H_sapiens_Feb_2009”.
genome(x)：获取基因组的名称，例如： “H_sapiens_Feb_2009”。
releaseDate(x): Get the release portion of the genome name, e.g., “Feb_2009”.
releaseDate(x)：释放部分基因组的名称，如“Feb_2009”。
organism(x): Get the organism portion of the genome name, e.g., “H sapiens”.
organism(x)：获取生物体基因组的名称部分，例如，“高智人”。
数据访问----------Data Access----------
length(x): number of datasets
length(x)：数据集
names(x), trackNames(x): names of the datasets
names(x), trackNames(x)：数据集的名称
elementMetadata(x): merged metadata on the datasets
elementMetadata(x)：合并数据集的元数据
track(x, name), x$name: get the track called name
track(x, name), x$name：name轨道
track(x, name, format = bestFileFormat(value), ...) <- value, x$name <- value: store the track value under name. Note that track storing is only supported for local repositories, i.e., those with a file:// URI scheme.
track(x, name, format = bestFileFormat(value), ...) <- value, x$name <- value：存储轨道value下name。请注意，跟踪存储只为本地资源库，即file://URI方案的支持。
Currently, supported value types include a GenomicRanges, GRangesList, or a file name (copied to the repository). 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.
目前，支持value类型包括GenomicRanges，GRangesList，或者一个文件名（复制到资料库）。如果不是一个文件名，value写在format。对于一般间隔数据，这意味着Bigwig的文件（如果有一个数字的“得分”栏），或一张床文件，否则。 RleList（例如，覆盖面）是作为Bigwig的输出。 UCSCData值，根据轨道线的类型，格式选择。 RsamtoolsFile对象，文件和它的索引被复制。
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.
...成为在XML元数据属性的参数。 “说明”属性是标准的，是描述在UI中的轨道1 Blurb的。对于剩下的解释是客户端。 IGB支持日益增长的名单，请参阅它的文档。
referenceSequence(x): Get the reference sequence, as a DNAStringSet.
referenceSequence(x)：DNAStringSet参考序列。
referenceSequence(x) <- value: Set the reference sequence, as a DNAStringSet. It is written as a 2bit file. This only works on local repositories.
referenceSequence(x) <- value：设置为参考序列，DNAStringSet。这是写一个2bit的文件。这仅适用于本地资源库。
作者（S）----------Author(s)----------
Michael Lawrence
举例----------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)
elementMetadata(qlg)
qlg$bedData
## Not run: [＃无法运行：]
## populating the test repository[＃填充测试库]
ql <- Quickload(file.path(tests_dir, "quickload")), create = TRUE)
reference_seq <- import(file.path(tests_dir, "test.2bit"))
names(reference_seq) <- "test"
qlg <- QuickloadGenome(ql, "T_species_Oct_2011", create = TRUE,
seqinfo = seqinfo(reference_seq))
referenceSequence(qlg) <- reference_seq
test_bed <- import(file.path(tests_dir, "test.bed"))
names(test_bed) <- "test"
qlg$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)[＃结束（不运行）]
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注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-2-26 13:39:34
