importFromAlignedReads(Genominator)
importFromAlignedReads()所属R语言包：Genominator
Import aligned reads to database
进口对齐读取到数据库
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function takes a named list of AlignedRead objects (from the ShortRead package) and creates an ExpData object from them, with one column for each list element. Column names
这个函数接受一个AlignedRead对象（ShortRead包）命名列表，并创建一个ExpData对象，从他们每个列表元素的一列。列名
用法----------Usage----------
importFromAlignedReads(x, chrMap, dbFilename,
tablename, overwrite = TRUE, deleteIntermediates = TRUE,
readPosition = c("5prime", "left", "center"),
verbose = getOption("verbose"), ...)
参数----------Arguments----------
参数：x
This argument can be one of two things: either a named list of objects of class AlignedRead or a named character vector of filenames. In both cases, the names of the object are used as column names inthe resulting database (not that it is not easy to change those names). Therefore the names of x needs to be present and non-empty and also to satisfy the requirements of column names in SQLite. If x is a list of AlignedRead, the column names needs to be unique. If x is a character vector of filenames, the names do not have to be unique, in which case two filenames with the same (column) name gets collapsed into the same column.
这个参数可以是一两件事情：无论是对象类AlignedRead或指定的字符向量文件名命名的名单。在这两种情况下，该对象的名称作为列名迟后产生的数据库（不，这是不容易改变这些名称）。因此名x需要，是当前和非空也SQLite中的列名，以满足要求。如果x是AlignedRead列表，列名必须是唯一的。如果x是一个文件名的字符向量，名不必须是唯一的，在这种情况下，两个具有相同的名称（列）的文件名进入同一列中倒塌。
参数：chrMap
A vector of chromosome names from the aligned output. On importation to the database, chromosome names will be converted to integers corresponding to position within the chrMap vector.
一个染色体的名字从对齐输出的向量。上输入到数据库中，染色体的名字将被转换为整数相应的位置在chrMap向量。
参数：dbFilename
The filename of the database to which the data will be imported.
其中的数据将被导入到数据库的文件名。
参数：tablename
Name of database table to write output data to.
输出数据写入数据库表名。
参数：overwrite
Logical indicating whether database table referred to in tablename argument should be overwritten.
逻辑说明中提到tablename参数应该是覆盖到数据库中的表是否。
参数：deleteIntermediates
Logical indicating whether intermediate database tables constructed in the process should be removed.
逻辑表示中间数据库建表的过程中是否应该被删除。
参数：readPosition
How each read is assigned a unique genomic location. Default is "5prime" indicating that the location is the position of the 5' end of the reads, "left" indicates that the position of the left part of the read is used (5' end for reads mapping to the forward strand, 3' for reads mapping to the reverse strand), "center" indicates that the position of the center of the read is used.
每读如何被分配一个独特的基因位置。默认是"5prime"说明该位置是5端的位置，读取，"left"表明（用于读取5端映射到左读的一部分的地位链，3映射到反向链读取），"center"表示，是用来读的中心位置。
参数：verbose
Logical indicating whether details should be printed.
逻辑说明是否应印有细节。
参数：...
Additional arguments to be passed to readAligned from ShortRead.
附加参数被传递到readAlignedShortRead。
Details
详情----------Details----------
The reads are aggregated and joined to form a database where each file/list element is a column. Positions are stored as the position of the 5' end of the reads (note that this differs from the convention for the AlignedRead class from ShortRead.) This can be changed by the readPosition argument.
读取汇总和加入，形成一个数据库，其中每个文件/列表元素是一列。位置存储读取的5端（注意，这从该公约的类AlignedRead。的ShortRead）不同，这可以通过改变readPosition参数的位置。
If the x argument is a character vector of filenames, the function will require enough memory to parse each input file in turn. If there are duplicates in names of x the function requires enough memory to parse all files with the same column name at the same time.
如果x参数是文件名的特征向量，函数将需要足够的内存，在每个输入文件解析。如果有重复的名字x的函数需要足够的内存来解析与在同一时间同一列名的所有文件。
If the AlignedRead class object has a weights column in its alignData slot, this weights column is used as the data to aggregate over.
如果AlignedRead类对象有一个weights列，其alignData插槽weights列用于数据合计超过。
值----------Value----------
Outputs an object of class ExpData with a column for each element of the x argument.
输出类对象ExpDatax参数中的每个元素的列。
作者（S）----------Author(s)----------
James Bullard <a href="mailto:bullard@berkeley.edu">bullard@berkeley.edu</a>,
Kasper Daniel Hansen <a href="mailto:khansen@jhsph.edu">khansen@jhsph.edu</a>
参见----------See Also----------
See Genominator vignette for more information. See also ExpData-class, AlignedRead-class and readAligned.
看到Genominator更多信息插曲。也见ExpData-class，AlignedRead-class和readAligned。
举例----------Examples----------
## Not run: [＃无法运行：]
require(ShortRead)
require(yeastRNASeq)
data("yeastAligned")
chrMap <- levels(chromosome(yeastAligned[[1]]))
eData <- importFromAlignedReads(yeastAligned, chrMap = chrMap,
dbFilename = tempfile(), tablename = "raw",
overwrite = TRUE)
## 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。
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发表于 2012-2-25 19:31:43
