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

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ShortReadQ-class(ShortRead)
ShortReadQ-class()所属R语言包：ShortRead

                                        "ShortReadQ" class for short reads and their quality scores
                                         类“ShortReadQ”的简称为读取和质量分数

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class provides a way to store and manipulate, in a coordinated fashion, the reads, identifiers, and quality scores of uniform-length short reads.
这个类提供的方式，以协调的方式，存储和操纵，读取，标识，统一长度短读取的质量分数。


类的对象----------Objects from the Class----------

Objects from this class are the result of readFastq, or can be constructed from DNAStringSet, QualityScore, and BStringSet objects, as described below.
从这个类的对象是readFastq的结果，或DNAStringSet，QualityScore，BStringSet对象，可以构造如下所述。


插槽----------Slots----------

Slots sread and id are inherited from ShortRead. An additional slot defined in this class is:
插槽sread和id是ShortRead继承。在这个类中定义一个额外的插槽是：




quality: Object of class "BStringSet" representing a quality score (see readFastq for some
quality：Object类的"BStringSet"代表的质量得分（见readFastq


延伸----------Extends----------

Class "ShortRead", directly. Class ".ShortReadBase", by class "ShortRead", distance 2.
类"ShortRead"，直接。类".ShortReadBase"，由类“ShortRead”，距离为2。


方法----------Methods----------

Constructors include:
构造包括：




ShortReadQ signature(sread = "DNAStringSet", quality = "QualityScore", id = "BStringSet"):
ShortReadQsignature(sread = "DNAStringSet", quality = "QualityScore", id = "BStringSet")：




ShortReadQ signature(sread = "DNAStringSet", quality = "BStringSet", id = "BStringSet"):
ShortReadQsignature(sread = "DNAStringSet", quality = "BStringSet", id = "BStringSet")：

Create a ShortReadQ object from reads, their quality scores, and identifiers. When quality is of class BStringSet, the type of encoded quality score is inferred from the letters used in the scores. The length of id and
创建ShortReadQ从读取对象，他们的质量分数，并标识。当quality类BStringSet，编码的质量得分的类型推断从分数中使用的字母。 id的长度和




ShortReadQ signature(sread = "DNAStringSet", quality = "QualityScore", id = "missing"):
ShortReadQsignature(sread = "DNAStringSet", quality = "QualityScore", id = "missing")：




ShortReadQ signature(sread = "DNAStringSet", quality = "BStringSet", id = "missing"):
ShortReadQsignature(sread = "DNAStringSet", quality = "BStringSet", id = "missing")：

Create a ShortReadQ object from reads and their quality scores, creating empty identifiers. When quality is of class BStringSet, the type of encoded quality score is
创建读取和其质量分数ShortReadQ对象，创建空的标识符。当quality类BStringSet，类型编码的质量得分




ShortReadQ signature(sread = "missing", quality = "missing", id = "missing", ...):
ShortReadQsignature(sread = "missing", quality = "missing", id = "missing", ...)：

See accessors for additional functions to access slot content, and ShortRead for inherited methods. Additional methods include:
看到accessors附加功能访问插槽含量，和ShortRead继承的方法。其他方法包括：




quality inherited from signature(object = "ANY"):
从signature(object = "ANY")质量继承：




coerce signature(from = "SFastqQuality", to = "QualityScaledDNAStringSet"):
强制signature(from = "SFastqQuality", to = "QualityScaledDNAStringSet")：

(Use as(from, "QualityScaledDNAStringSet")) coerce objects of class from to class to, using the quality encoding implied by quality(from). See QualityScore for supported quality
（使用as(from, "QualityScaledDNAStringSet")）要挟类对象from类to，quality(from)使用的质量编码暗示。看到QualityScore支持的质量




writeFastq signature(object = "ShortReadQ", file =
writeFastq的<code>签名（对象=“ShortReadQ”，文件=




writeFastq signature(object = "ShortReadQ", file =         "FastqFile", ...): Write object to file in fastq format. See ?writeFastq for additional arguments mode
writeFastqsignature(object = "ShortReadQ", file =         "FastqFile", ...)：写objectfilefastq格式。 额外的参数?writeFastqmode




[ signature(x = "ShortReadQ", i = "ANY", j = "missing"):  This method creates a new ShortReadQ object containing only those reads indexed by i. Additional methods on "[,ShortRead" do not provide additional functionality, but
[signature(x = "ShortReadQ", i = "ANY", j = "missing")：此方法创建一个新的ShortReadQ对象，其中包含只有那些索引读取i。额外的方法“，ShortRead不提供额外的功能，但




append signature(x = "ShortReadQ", values = "ShortRead", length = "missing"): append the sread, quality and id slots of
追加signature(x = "ShortReadQ", values = "ShortRead", length = "missing")：sread，quality和id槽追加




narrow signature(x = "ShortReadQ", start = NA, end =       NA, width = NA, use.names = TRUE): narrow sread and quality so that sequences are between start and end bases, according to narrow in the IRanges
窄signature(x = "ShortReadQ", start = NA, end =       NA, width = NA, use.names = TRUE)：窄sread和quality使序列之间start和end碱基，根据narrowIRanges




trimTailw signature(object="ShortReadQ", k="integer",         a="character", halfwidth="integer", ..., ranges=FALSE): trim trailing nucleotides when a window of width 2 * halfwidth + 1 contains k or more quality scores falling at or below
当一个窗口宽度2 *半角+ 1包含signature(object="ShortReadQ", k="integer",         a="character", halfwidth="integer", ..., ranges=FALSE)或更多的质量分数下降或低于trimTailwk：修剪尾随核苷酸




trimTails signature(object="ShortReadQ", k="integer",         a="character", successive=FALSE, ..., ranges=FALSE): trim trailing nucleotides if k nucleotides fall below the quality encoded by a. If successive=FALSE, the k'th failing nucleotide and all subseqent nucleotides are trimmed. If successive=TRUE, failing nucleotides must occur successively; the sequence is trimmed from the first of the
trimTailssignature(object="ShortReadQ", k="integer",         a="character", successive=FALSE, ..., ranges=FALSE)：修剪尾随核苷酸k核苷酸如果低于a编码的质量下降。如果successive=FALSE，第k个失败的核苷酸和subseqent核苷酸修剪。如果successive=TRUE，未能核苷酸必须先后发生的顺序是从第一次修剪




alphabetByCycle signature(stringSet = "ShortReadQ"): Apply alphabetByCycle to the sread component, the quality component, and the combination of these two components of stringSet, returning a list of matrices with three elements: "sread", "quality", and
alphabetByCyclesignature(stringSet = "ShortReadQ")：申请alphabetByCycle组件sread，quality组件，这两个组件stringSet，返回一个列表矩阵的组合三个要素："sread"，"quality"，




alphabetScore signature(object = "ShortReadQ"):
alphabetScoresignature(object = "ShortReadQ")：




qa signature(dirPath = "ShortReadQ", lane="character",         ..., verbose=FALSE): Perform quality assessment on the ShortReadQ object using lane to identify the object and returning an instance of
QAsignature(dirPath = "ShortReadQ", lane="character",         ..., verbose=FALSE)：ShortReadQ使用对象执行质量评估lane物色对象，并返回一个实例




detail signature(x = "ShortReadQ"): display the first and last entries of each of sread, id, and
详细signature(x = "ShortReadQ")：显示第一个和最后一个条目，每个sreadid，


作者（S）----------Author(s)----------


Martin Morgan



参见----------See Also----------

readFastq for creation of objects of this class from fastq-format files.
readFastq创造这一类从fastq格式文件的对象。


举例----------Examples----------


showClass("ShortReadQ")
showMethods(class="ShortReadQ", where=getNamespace("ShortRead"),
            inherit=FALSE)
showMethods(class="ShortRead", where=getNamespace("ShortRead"),
            inherit=FALSE)

sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
quality(rfq)
quality(trimTails(rfq, 2, "H", successive=TRUE))

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