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

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trimTails(ShortRead)
trimTails()所属R语言包：ShortRead

                                        Trim ends of reads based on nucleotides or qualities
                                         根据核苷酸或品质读取修剪完

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

These generic functions remove leading or trailing nucleotides or qualities. trimTails and trimTailw remove low-quality reads from the right end using a sliding window (trimTailw) or a tally of (successive) nucleotides falling at or below a quality threshold (trimTails). trimEnds takes an alphabet of characters to remove from either left or right end.
这些通用功能删除前导或尾随核苷酸或品质。 trimTails和trimTailw从低质量，正确使用一个滑动窗口（trimTailw）或（连续）或以下的质量阈值（下降核苷酸相符读取<X >）。 trimTails需要一个字母字符，删除或左或右的结束。


用法----------Usage----------


trimTailw(object, k, a, halfwidth, ..., ranges=FALSE)

## S4 method for signature 'BStringSet'
trimTailw(object, k, a, halfwidth, ..., alphabet, ranges=FALSE)
## S4 method for signature 'XStringQuality'
trimTailw(object, k, a, halfwidth, ..., ranges=FALSE)

trimTails(object, k, a, successive=FALSE, ..., ranges=FALSE)
## S4 method for signature 'BStringSet'
trimTails(object, k, a, successive=FALSE, ...,
    alphabet, ranges=FALSE)
## S4 method for signature 'XStringQuality'
trimTails(object, k, a, successive=FALSE, ..., ranges=FALSE)

trimEnds(object, a, left=TRUE, right=TRUE, relation=c("&lt;=", "=="),
    ..., ranges=FALSE)
## S4 method for signature 'XStringSet'
trimEnds(object, a, left=TRUE, right=TRUE, relation=c("&lt;=", "=="),
    ..., ranges=FALSE)
## S4 method for signature 'XStringQuality'
trimEnds(object, a, left=TRUE, right=TRUE, relation=c("&lt;=", "=="),
    ..., ranges=FALSE)
## S4 method for signature 'FastqQuality'
trimEnds(object, a, left=TRUE, right=TRUE, relation=c("&lt;=", "=="),
    ..., ranges=FALSE)
## S4 method for signature 'ShortRead'
trimEnds(object, a, left=TRUE, right=TRUE, relation=c("&lt;=", "=="),
    ..., ranges=FALSE)
## S4 method for signature 'ShortReadQ'
trimEnds(object, a, left=TRUE, right=TRUE, relation=c("&lt;=", "=="),
    ..., ranges=FALSE)



参数----------Arguments----------

参数：object
An object for which a methods exist (e.g., ShortReadQ and derived classes); see below to discover these methods.
一个对象的方法存在（例如，ShortReadQ和派生类）;看到下面发现这些方法。


参数：k
integer(1) describing the number of failing letters required to trigger trimming.
integer(1)描述触发修剪未能字母的数目。


参数：a
For trimTails and trimTailw, a character(1) with nchar(a) == 1L giving the letter at or below which a nucleotide is marked as failing.  For trimEnds a character() with all nchar() ==     1L giving the letter at or below which a nucleotide or quality scores marked for removal.
trimTails和trimTailw，character(1)nchar(a) == 1L给予或低于核苷酸的字母标记为失败。 trimEndscharacter()都nchar() ==     1L信或低于去除标记的核苷酸或质量分数。


参数：halfwidth
The half width (cycles before or after the current; e.g., a half-width of 5 would span 5 + 1 + 5 cycles) in which qualities are assessed.
半宽度（周期之前或之后的电流，例如，半宽5跨5 + 1 + 5个周期），其中素质评估。


参数：successive
logical(1) indicating whether failures can occur anywhere in the sequence, or must be successive. If successive=FALSE, then the k'th failed letter and subsequent are removed. If successive=TRUE, the first succession of k failed and subsequent letters are removed.
logical(1)表示失败是否可以序列中的任何地方发生，或必须是连续的。如果successive=FALSE，则第k个失败的信和随后被删除。如果successive=TRUEk的第一继承失败和随后的信件被删除。


参数：left, right
logical(1) indicating whether trimming is from the left or right ends.
logical(1)指示是否修剪是左或右两端。


参数：relation
character(1) selected from the argument values, i.e., &ldquo;<=&rdquo; or &ldquo;==&rdquo; indicating whether all letters at or below the alphabet(object) are to be removed, or only exact matches.
character(1)从选定的参数值，即“<=”或“==”表示所有的字母是否等于或低于alphabet(object)将被删除，或者只精确匹配。


参数：...
Additional arguments, perhaps used by methods.
额外的参数，也许使用的方法。


参数：alphabet
character() (ordered low to high) letters on which quality scale is measured. Usually supplied internally (user does not need to specify). If missing, then set to ASCII characters 0-127.
character()（有序低到高），上规模是衡量质量的信件。一般提供内部（不需要用户指定）。如果失踪，然后设置为0-127的ASCII字符。


参数：ranges
logical(1) indicating whether the trimmed object, or only the ranges satisfying the trimming condition, be returned.
logical(1)指示是否修剪的对象，或只修剪条件满足的范围，返回。


Details

详情----------Details----------

trimTailw starts at the left-most nucleotide, tabulating the number of cycles in a window of 2 * halfwidth + 1 surrounding the current nucleotide with quality scores that fall at or below a. The read is trimmed at the first nucleotide for which this number >= k. The quality of the first or last nucleotide is used to represent portions of the window that extend beyond the sequence.
trimTailw开始在最左边的核苷酸，在一个窗口2 * halfwidth + 1周围的质量分数下降或低于a核苷酸制表的周期数。读的第一个核苷酸这>= k修剪。用来表示窗口的序列超出部分的第一个或最后一个核苷酸的质量。

trimTails starts at the left-most nucleotide and accumulates cycles for which the quality score is at or below a. The read is trimmed at the first location where this number >= k. With successive=TRUE, failing qualities must occur in strict succession.
trimTails开始在最左边的核苷酸和积累的周期，而质量得分或低于a。读修剪在第一的位置，这个数字>= k。与successive=TRUE，没有素质，必须发生在严格继承。

trimEnds examines the left, right, or both ends of object, marking for removal letters that correspond to a and relation. The trimEnds,ShortReadQ-method trims based on quality.
trimEnds检查left，right或object两端，去除字母对应a和relation标记。 trimEnds,ShortReadQ-method质量为基础修剪。


值----------Value----------

An instance of class(object) trimmed to contain only those nucleotides satisfying the trim criterion or, if ranges=TRUE an IRanges instance defining the ranges that would trim object.
一个class(object)实例修剪，只包含那些满足修剪标准的核苷酸或如果ranges=TRUEIRanges实例定义的范围，将削减object。


作者（S）----------Author(s)----------


Martin Morgan &lt;mtmorgan@fhcrc.org&gt;



举例----------Examples----------


showMethods(trimTails)

sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")

## remove leading / trailing quality scores &lt;= 'I'[＃删除前导/尾随质量分数<=我]
trimEnds(rfq, "I")
## remove leading / trailing 'N's[＃删除前导/尾随“N]
rng <- trimEnds(sread(rfq), "N", relation="==", ranges=TRUE)
narrow(rfq, start(rng), end(rng))
## remove leading / trailing 'G's or 'C's[＃删除前导/尾随G的或“C”]
trimEnds(rfq, c("G", "C"), relation="==")


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