makeTxDbPackage(GenomicFeatures)
makeTxDbPackage()所属R语言包：GenomicFeatures
Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source.
1 TranscriptDb包注释在UCSC基因组浏览器，biomaRt或从其他来源。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The makeTxDbPackageFromUCSC function allows the user to make a TranscriptDb object from transcript annotations available at the UCSC Genome Browser. The makeTxDbPackageFromBiomart function allows the user to do the same thing as makeTxDbPackageFromUCSC except that the annotations originate from biomaRt. Finally, the makeTxDbPackage function allows the user to make a TranscriptDb object from transcript annotations that are in a custom transcript Database, such as could be produced using makeTranscriptDb.
makeTxDbPackageFromUCSC功能允许用户从UCSC基因组浏览器提供的成绩单注释TranscriptDb对象。 makeTxDbPackageFromBiomart功能，使用户可以做同样的事情makeTxDbPackageFromUCSC除了注释从biomaRt起源。最后，makeTxDbPackage功能允许用户从一个自定义的谈话全文数据库的成绩单注释1 TranscriptDb对象，如可以生产使用makeTranscriptDb。
用法----------Usage----------
makeTxDbPackageFromUCSC(
version=,
maintainer,
author,
destDir=".",
license="Artistic-2.0",
genome="hg19",
tablename="knownGene",
transcript_ids=NULL,
circ_seqs=DEFAULT_CIRC_SEQS,
url="http://genome.ucsc.edu/cgi-bin/",
goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath")
makeTxDbPackageFromBiomart(
version,
maintainer,
author,
destDir=".",
license="Artistic-2.0",
biomart="ensembl",
dataset="hsapiens_gene_ensembl",
transcript_ids=NULL,
circ_seqs=DEFAULT_CIRC_SEQS)
makeTxDbPackage(txdb,
version,
maintainer,
author,
destDir=".",
license="Artistic-2.0")
参数----------Arguments----------
参数：version
What is the version number for this package?
这个包的版本号是什么？
参数：maintainer
Who is the package maintainer? (must include email to be valid)
软件包的维护者是谁？ （必须是有效的，包括电子邮件）
参数：author
Who is the creator of this package?
这个包的创建者是谁？
参数：destDir
A path where the package source should be assembled.
一个包的源路径应组装。
参数：license
What is the license (and it's version)
什么是许可证（和它的版本）
参数：biomart
which BioMart database to use. Get the list of all available BioMart databases with the listMarts function from the biomaRt package. See the details section below for a list of BioMart databases with compatible transcript annotations.
使用其中BioMart的数据库。获取listMarts从biomaRt包功能所有可用BioMart数据库列表。与兼容的成绩单注释BioMart数据库列表，请参见下面的详细信息部分。
参数：dataset
which dataset from BioMart. For example: "hsapiens_gene_ensembl", "mmusculus_gene_ensembl", "dmelanogaster_gene_ensembl", "celegans_gene_ensembl", "scerevisiae_gene_ensembl", etc in the ensembl database. See the examples section below for how to discover which datasets are available in a given BioMart database.
其中集从BioMart。例如："hsapiens_gene_ensembl"，"mmusculus_gene_ensembl"，"dmelanogaster_gene_ensembl"，"celegans_gene_ensembl"，"scerevisiae_gene_ensembl"，在ENSEMBL数据库等。请参阅如何发现数据集是在一个给定的BioMart数据库的例子，下面一节。
参数：genome
genome abbreviation used by UCSC and obtained by ucscGenomes()[ , "db"]. For example: "hg18".
基因组的缩写，由加州大学圣克鲁兹分校和获得ucscGenomes()[ , "db"]。例如："hg18"。
参数：tablename
name of the UCSC table containing the transcript annotations to retrieve. Use the supportedUCSCtables utility function to get the list of supported tables. Note that not all tables are available for all genomes.
UCSC的包含谈话注解检索的表的名称。使用supportedUCSCtables实用功能得到支持的表的列表。请注意，并非所有的表可用于所有基因组。
参数：transcript_ids
optionally, only retrieve transcript annotation data for the specified set of transcript ids. If this is used, then the meta information displayed for the resulting TranscriptDb object will say 'Full dataset: no'. Otherwise it will say 'Full dataset: yes'.
选择性，只检索指定的一组转录IDS的成绩单注释数据。如果这是用来显示产生TranscriptDb对象的元信息会说：“完整的数据集：没有”。否则，它会说“全部数据集：有。
参数：circ_seqs
a character vector to list out which chromosomes should be marked as circular.
字符向量，列出染色体应为圆形标记。
参数：url,goldenPath_url
use to specify the location of an alternate UCSC Genome Browser.
使用指定备用UCSC基因组浏览器的位置。
参数：txdb
A TranscriptDb object that represents a handle to a transcript database. This object type is what is returned by makeTranscriptDbFromUCSC, makeTranscriptDbFromUCSC or makeTranscriptDb
一个TranscriptDb代表以誊数据库句柄对象。这个对象的类型是什么makeTranscriptDbFromUCSC，makeTranscriptDbFromUCSC或makeTranscriptDb返回
Details
详情----------Details----------
makeTxDbPackageFromUCSC is a convenience function that calls both the makeTranscriptDbFromUCSC and the makeTxDbPackage functions. The makeTxDbPackageFromBiomart follows a similar pattern and calls the makeTranscriptDbFromBiomart and makeTxDbPackage functions.
makeTxDbPackageFromUCSC是一个方便的功能，称之为makeTranscriptDbFromUCSC“makeTxDbPackage功能。 makeTxDbPackageFromBiomart遵循类似的模式，并呼吁makeTranscriptDbFromBiomart和makeTxDbPackage功能。
值----------Value----------
A TranscriptDb object.
TranscriptDb对象。
作者（S）----------Author(s)----------
M. Carlson
参见----------See Also----------
ucscGenomes, DEFAULT_CIRC_SEQS, makeTranscriptDbFromUCSC, makeTranscriptDbFromBiomart, makeTranscriptDb
ucscGenomes，DEFAULT_CIRC_SEQS，makeTranscriptDbFromUCSC，makeTranscriptDbFromBiomart，makeTranscriptDb
举例----------Examples----------
## Display the list of tables supported by makeTxDbPackageFromUCSC():[＃显示表由makeTxDbPackageFromUCSC（）支持列表：]
supportedUCSCtables()
## Not run: [＃无法运行：]
## Makes a transcript package for Yeast from the ensGene table at UCSC:[＃使得从UCSC的ensGene的表酵母成绩单，包：]
makeTxDbPackageFromUCSC(version="0.01",
maintainer="Some One <so@someplace.org>",
author="Some One <so@someplace.com>",
genome="sacCer2",
tablename="ensGene")
## Makes a transcript package from Human by using biomaRt and limited to a [＃使人权成绩单包通过使用biomaRt从限于]
## small subset of the transcripts.[＃一小部分的成绩单。]
transcript_ids <- c(
"ENST00000400839",
"ENST00000400840",
"ENST00000478783",
"ENST00000435657",
"ENST00000268655",
"ENST00000313243",
"ENST00000341724")
makeTxDbPackageFromBiomart(version="0.01",
maintainer="Some One <so@someplace.org>",
author="Some One <so@someplace.com>",
transcript_ids=transcript_ids)
## End(Not run)[＃结束（不运行）]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 19:27:26
