deprecated(ShortRead)
deprecated()所属R语言包：ShortRead
Deprecated and defunct functions
过时和解散的功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These functions were introduced but are now deprecated or defunct.
这些功能进行了介绍，但现在已经过时或倒闭。
用法----------Usage----------
basePath(object, ...)
pileup(start, fraglength, chrlength, dir = strand( "+" ),
readlength = fraglength, offset = 1)
参数----------Arguments----------
参数：object
For basePath, and object of class ExperimentPath.
对于basePath类ExperimentPath对象。
参数：...
Additional arguments.
额外的参数。
参数：start
A vector with the start positions of each read on the reference sequence. All reads must correspond to the same reference sequence.
每个读的参考序列的起始位置的向量。所有读取数据必须符合相同的参考序列。
参数：fraglength
A vector of the same length as 'start' with the lengths of all the fragments. Alternatively, a single integer, specifying one constant length to assume for all tags.
开始的所有片段的长度为相同长度的向量。另外，一个整数，指定一个固定长度承担所有标签。
参数：chrlength
The length of the reference sequence. You may use the function readBfaToc to extract this information from the .bfa file.
参考序列的长度。你可以使用的功能readBfaToc。博鳌亚洲论坛文件中提取信息。
参数：dir
A factor with level "-" and "+" of the same length as 'start', specifying whether the fragment extends to the right (towards higher index values, '+') or to the left (towards lower index values, '-') beyond the read. See below for more explanation.
同级别的因素“ - ”和“+”开始的长度相同，指定片段是否延伸到的权利（对更高的指数值，“+”）或向左（向低指数值， - ）之外的阅读。更多的解释见下文。
参数：readlength
The length of the reads, either as a vector of the same length as 'start' or as a single number. This parameter makes sense only if 'dir' is used, too. If not specified, read lengths and fragment lengths are taken to be the same.
在读取的长度，无论是作为“开始”，或作为一个单一的数字相同长度的向量。此参数使得只有使用“目录”的感觉，太。如果没有指定，读取长度和片段的长度是相同的。
参数：offset
The index of the first base pair in the result vector. The default is 1, i.e. assumes that the 'start' positions are in 1-based chromosome coordinates.
结果向量的第一个碱基对的指数。默认值是1，即假设“开始的位置是在1号染色体的坐标。
值----------Value----------
参数：<code>pileup</code>
an integer vector of length 'chrlength', each element counting how many fragments map to this basepair.
一个长度chrlength的整数向量，每个元素的计数多少片段映射到这个碱基。
注意----------Note----------
(the following refers to the pileup function)
（以下是指pileup功能）
1. This function is not suitable for paired-end reads.
1。这个功能是不适合的配对末端读取。
2. If the arguments 'dir' and 'readlength' are not used, the fragments are assumed to start at the positions given in 'start' and extend to the right by the number of basepairs given in fraglength. If 'dir' and 'readlength' are supplied then the interval starting at 'start' and extending to the right by the number of base pairs given in 'readlength' marks the position of the read, which is one end of the fragment. If 'dir' ist '+', it is taken as the left end and the fragment will be extended to the right to have the total length given by 'fraglength'. If 'dir' is '-', the end is taken as the right end and is extended to the left. Note that in the latter case, the 'start' position does mark the border between read and rest of fragment, not an actual 'end' of the fragment. If you are confused now, look at the examples below.
2。如果不使用参数目录和readlength“，片段假设开始在开始的立场，并延长在fraglength给予碱基数量的权利。如果“目录”和“readlength”提供的时间间隔，然后在“开始”开始，并扩展到右边readlength“给定的碱基对数目，标志着读的位置，这是一个片段结束。如果“目录”IST“+”，它被视为左端和片段将扩大到有权有总长度给fraglength。如果目录是 - ，到底是采取正确的结束，并延伸到左。请注意，在后一种情况下，“开始”位置标记读取和截断的片段，而不是一个实际的“结束”的片段之间的边界。如果你现在的困惑，看看下面的例子。
3. Sorry for the inconsequent use of 'width' and 'length' in a seemingly interchangeable fashion.
3。对不起宽和长在一个看似互换的方式inconsequent使用。
作者（S）----------Author(s)----------
Simon Anders, EMBL-EBI, <a href="mailto:sanders@fs.tum.de">sanders@fs.tum.de</a>
举例----------Examples----------
Example 1: Assuming that 'lane' is an 'AlignedRead' object containing
aligned reads from a Solexa lane, you may get a pile-up representation
of chromosome 13 as follows
chr13length <- 114142980 # the length of human chromosme 13[人类chromosme 13的长度]
pu <- pileup(position(lane)[chromosome(lane)=="13"],
width(lane), chr13length )
Example 2: Even though the width of the reads (as repored by
'width(lane)') is only 24, these 24 bp are just one end of a longer
fragment. Assuming that all fragments have been sonicated to about the
same length, say 150 bp, we may get a better pile-up representation by:
pu2 <- pileup(position(lane)[chromosome(lane)=="13"], 150,
chr13length, strand(lane)[chromosome(lane)=="13"],
width(lane) )
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 2012-2-26 14:04:05
