R语言 GenomicFeatures包 makeFeatureDbFromUCSC()函数中文帮助文档(中英文对照)

loveR

makeFeatureDbFromUCSC(GenomicFeatures)
makeFeatureDbFromUCSC()所属R语言包：GenomicFeatures

                                         Making a FeatureDb object from annotations available at the UCSC Genome Browser
                                         在UCSC基因组浏览器提供的注释1 FeatureDb对象

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

The makeFeatureDbFromUCSC function allows the user to make a FeatureDb object from simple annotation tracks at UCSC.  The tracks in question must (at a minimum) have a start, end and a chromosome affiliation in order to be made into a FeatureDb. This function requires a precise declaration of its first three arguments to indicate which genome, track and table wish to be imported.  There are discovery functions provided to make this process go smoothly.
makeFeatureDbFromUCSC功能允许用户从简单的注解轨道在UCSC FeatureDb对象的。问题的轨道，必须至少有一个起点，终点和染色体的联系，以取得成FeatureDb。此功能需要一个精确的声明，表明基因组，跟踪和表希望将进口其前三个参数。有提供发现功能，使这个过程顺利。


用法----------Usage----------


supportedUCSCFeatureDbTracks(genome)

supportedUCSCFeatureDbTables(genome, track)

UCSCFeatureDbTableSchema(genome,
                         track,
                         tablename)

makeFeatureDbFromUCSC(
        genome,
        track,
        tablename,
        columns = UCSCFeatureDbTableSchema(genome,track,tablename),
        url="http://genome.ucsc.edu/cgi-bin/",
        goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath",
        chromCol,
        chromStartCol,
        chromEndCol)



参数----------Arguments----------

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：track
name of the UCSC track.  Use supportedUCSCFeatureDbTracks to get the list of available tracks for a particular genome
UCSC的曲目名称。使用supportedUCSCFeatureDbTracks得到一个特定的基因组可用的轨道列表


参数：tablename
name of the UCSC table containing the annotations to retrieve. Use the supportedUCSCFeatureDbTables utility function to get the list of supported tables for a track.
UCSC的包含注释检索的表的名称。使用supportedUCSCFeatureDbTables效用函数得到的轨道支持的表的列表。


参数：columns
a named character vector to list out the names and types of the other columns that the downloaded track should have.  Use UCSCFeatureDbTableSchema to retrieve this information for a particular table.
一个命名的特征向量，列出下载的曲目应该有其他列的名称和类型。使用UCSCFeatureDbTableSchema到一个特定的表中检索这些信息。


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：chromCol
If the schema comes back and the 'chrom' column has been  labeled something other than 'chrom', use this argument to indicate  what that column has been labeled as so we can properly designate it. This could happen (for example) with the knownGene track tables, which has no 'chromStart' or 'chromEnd' columns, but which DOES have columns that could reasonably substitute for these columns under particular  circumstances.  Therefore we allow these three columns to have arguments so that their definition can be re-specified
如果架构回来，“铬”列已贴上“铬”以外的其他的东西，使用这个参数表明该列已贴上什么，所以我们可以正确地指定它。可能会发生这种情况（例如）的knownGene跟踪表，其中有没有“chromStart或chromEnd”列，但它有列，这些列在特定情况下可以合理替代。因此，我们允许这三列，使他们重新定义可以指定的参数


参数：chromStartCol
Same thing as chromCol, but for renames of 'chromStart'
同样的事情作为chromCol，但“chromStart”改名


参数：chromEndCol
Same thing as chromCol, but for renames of 'chromEnd'
同样的事情作为chromCol，但“chromEnd”改名


Details

详情----------Details----------

makeFeatureDbFromUCSC is a convenience function that builds a tiny database from one of the UCSC track tables. supportedUCSCFeatureDbTracks a convenience function that returns potential track names that could be used to make FeatureDb objects supportedUCSCFeatureDbTables a convenience function that returns potential table names for FeatureDb objects (table names go with a track name) UCSCFeatureDbTableSchema A convenience function that creates a named vector of types for all the fields that can potentially be supported for a given track.  By default, this will be called on your specified tablename to include all of the fields in a track.
makeFeatureDbFromUCSC是一个方便的功能，建立一个小的数据库，从UCSC的曲目表。 supportedUCSCFeatureDbTracks一个方便的函数返回跟踪潜在的名称，可以用来做FeatureDb对象supportedUCSCFeatureDbTables一个方便的功能，潜在的表名返回FeatureDb对象（表名称与曲目名称）UCSCFeatureDbTableSchema一项方便的功能，创建一个给定的轨道，可能会被用于支持所有字段命名为向量的类型。默认情况下，这将被称为对你指定的表名，包括所有在轨道领域。


值----------Value----------

A FeatureDb object for makeFeatureDbFromUCSC.  Or in the case of supportedUCSCFeatureDbTracks and
一个的makeFeatureDbFromUCSCFeatureDb对象。或者在supportedUCSCFeatureDbTracks“的情况下


作者（S）----------Author(s)----------



M. Carlson and H. Pages




参见----------See Also----------

ucscGenomes,  
ucscGenomes


举例----------Examples----------


## Display the list of genomes available at UCSC:[＃显示在UCSC基因组名单：]
library(GenomicFeatures)
library(rtracklayer)
ucscGenomes()[ , "db"]

## Display the list of Tracks supported by makeFeatureDbFromUCSC():[＃显示由makeFeatureDbFromUCSC（）支持的曲目列表：]
supportedUCSCFeatureDbTracks("mm9")

## Display the list of tables supported by your track:[＃显示您的轨道支持的表的列表：]
supportedUCSCFeatureDbTables(genome="mm9",
                             track="oreganno")

## Display fields that could be passed in to colnames:[＃显示，可以通过在colnames领域：]
UCSCFeatureDbTableSchema(genome="mm9",
                         track="oreganno",
                         tablename="oreganno")

## Retrieving a full transcript dataset for Yeast from UCSC:[＃检索完整记录的数据集，从加州大学圣克鲁兹分校的酵母：]
fdb <- makeFeatureDbFromUCSC(genome="mm9",
                              track="oreganno",
                              tablename="oreganno")
fdb


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。