QualityScore-class(ShortRead)
QualityScore-class()所属R语言包：ShortRead
Quality scores for short reads and their alignments
质量分数为短读取和他们的路线
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class hierarchy represents quality scores for short reads. QualityScore is a virtual base class, with derived classes offering different ways of representing qualities. Methods defined on QualityScore are implemented in all derived classes.
代表短期读取这个类层次的质量分数。 QualityScore是一个虚基类，派生类提供不同的方式代表素质。 QualityScore定义的方法是所有派生类中实现。
类的对象----------Objects from the Class----------
Objects from the class are created using constructors (e.g., NumericQuality) named after the class name.
从类创建对象使用构造（例如，NumericQuality）类的名称命名。
Defined classes are as follows:
定义的类如下：
QualityScore Virtual base class; instances cannot be
QualityScore虚拟基类的实例不能
NumericQuality A single numeric vector, where values
NumericQuality一个数字向量，其中值
IntegerQuality A integer numeric vector, where values
IntegerQuality一个整数的数字向量，其中值
MatrixQuality A rectangular matrix of quality scores, with rows representing reads and columns cycles. The content and interpretation of row and column entries is arbitrary; the rectangular nature implies quality scores from equal-length
MatrixQuality的质量分数的长方形矩阵，行代表读取和列周期。行和列项的内容和解释是任意矩形的性质意味着从长度相等的质量分数
FastqQuality "fastq" encoded quality scores stored in a BStringSet instance. Base qualities of a single read are represented as an ASCII character string. The integer-valued quality score of a single base is encoded as its ASCII equivalent plus 33. The precise definition of the integer-valued quality score is unspecified, but is usually a Phred score; the meaning can be determined from the source of the quality scores. Multiple reads are stored as a BStringSet, and so can be of varying
BStringSet实例存储在“fastq”FastqQuality编码质量分数。作为ASCII字符串表示一个读取相应的素质。整数值的质量得分的一个单一的碱基被编码为ASCII等效加33。确切的定义的整数值的质量得分是不确定的，但通常是一个PHRED得分的含义可以从源的质量分数确定。多次读取存储作为一个BStringSet，所以可以是不同
SolexaQuality As with FastqQuality, but with integer
SolexaQualityFastqQuality，但与整数
延伸----------Extends----------
Class ".ShortReadBase", directly.
类".ShortReadBase"，直接。
方法----------Methods----------
The following methods are defined on all QualityScore and derived classes:
所有QualityScore和派生类定义下列方法：
[ signature(x = "QualityScore", i = "ANY", j = "missing")
[signature(x = "QualityScore", i = "ANY", j = "missing")
[ signature(x = "MatrixQuality", i = "ANY", j = "missing"):
[signature(x = "MatrixQuality", i = "ANY", j = "missing")：
Subset the object, with index i indicating the reads for which quality scores are to be extracted. The class of the result is the same as the class of x. It is an error to provide
子集的对象，与指数i表明读取的质量分数是要提取。类的结果是相同的类x的。这是一个错误提供
[[ signature(x = "QualityScore", i = "ANY", j = "ANY"):
[signature(x = "QualityScore", i = "ANY", j = "ANY")：
Subset the object, returning the quality score (e.g., numeric
子集的对象，返回的质量得分（例如，数字
[[ signature(x = "MatrixQuality", i = "ANY", j = "ANY"):
[signature(x = "MatrixQuality", i = "ANY", j = "ANY")：
Returns the vector of quality scores associated with the
返回的向量与相关的质量分数
dim signature(x = "MatrixQuality"):
昏暗的signature(x = "MatrixQuality")：
The integer(2) dimension (e.g., number of reads, read width)
整数（2）尺寸（例如，读取数量，读取宽度）
length signature(x = "QualityScore"):
长度signature(x = "QualityScore")：
length signature(x = "MatrixQuality"):
长度signature(x = "MatrixQuality")：
The integer(1) length (e.g., number of reads) represented by the quality score. Note that length of MatrixQuailty is the number of rows of the corresponding matrix, and not the length
整数（1）长度（例如，读取数）的质量得分表示。请注意，lengthMatrixQuailty相应的矩阵的行的数目，而不是长度
append signature(x = "QualityScore", values = "QualityScore", length = "missing"):
追加signature(x = "QualityScore", values = "QualityScore", length = "missing")：
width signature(x = "QualityScore"):
宽度signature(x = "QualityScore")：
width signature(x = "NumericQuality"):
宽度signature(x = "NumericQuality")：
width signature(x = "MatrixQuality"):
宽度signature(x = "MatrixQuality")：
width signature(x = "FastqQuality"):
宽度signature(x = "FastqQuality")：
A numeric vector with length equal to the number of quality scores, and value equal to the number of quality scores for each read. For instance, a FastqQuality will have widths equal to the number of nucleotides in the underlying short read.
一个长度等于质量分数，质量分数为每个读值等于数字向量。例如，FastqQuality将有宽度等于底层短读的核苷酸数量。
show signature(object = "QualityScore"):
显示signature(object = "QualityScore")：
show signature(object = "NumericQuality"):
显示signature(object = "NumericQuality")：
show signature(object = "FastqQuality"):
显示signature(object = "FastqQuality")：
provide a brief summary of the object content.
提供了一个对象的内容简要。
detail signature(x = "QualityScore"):
详细signature(x = "QualityScore")：
provide a more detailed view of object content.
提供更详细的视图对象的内容。
The following methods are defined on specific classes:
以下方法是在特定的类定义：
alphabet signature(x = "FastqQuality", ...): Return a character vector of valid quality characters.
字母表signature(x = "FastqQuality", ...)：返回一个有效的品质性状的特征向量。
alphabetFrequency signature(stringSet = "FastqQuality"):
alphabetFrequencysignature(stringSet = "FastqQuality")：
Apply alphabetFrequency to quality scores, returning a matrix as described in
申请alphabetFrequency质量分数，返回一个矩阵中所述
alphabetByCycle signature(stringSet = "FastqQuality"):
alphabetByCyclesignature(stringSet = "FastqQuality")：
Apply alphabetByCycle to quality scores, returning a
申请alphabetByCycle质量分数，返回
alphabetScore signature(object = "FastqQuality"):
alphabetScoresignature(object = "FastqQuality")：
alphabetScore signature(object = "SFastqQuality"):
alphabetScoresignature(object = "SFastqQuality")：
Apply alphabetScore (i.e., summed base quality, per
申请alphabetScore（即总结的基础质量，每
coerce signature(from = "FastqQuality", to = "numeric"):
强制signature(from = "FastqQuality", to = "numeric")：
coerce signature(from = "FastqQuality", to = "matrix"):
强制signature(from = "FastqQuality", to = "matrix")：
coerce signature(from = "FastqQuality", to = "PhredQuality"):
强制signature(from = "FastqQuality", to = "PhredQuality")：
coerce signature(from = "SFastqQuality", to = "matrix"):
强制signature(from = "SFastqQuality", to = "matrix")：
coerce signature(from = "SFastqQuality", to = "SolexaQuality"):
强制signature(from = "SFastqQuality", to = "SolexaQuality")：
Use like as(from, "matrix")) to coerce objects of class from to class to, using the quality encoding implied by the class. When to is “matrix”, all quality scores must be of the same width, and the result is a matrix of type integer. The result always represents the
像as(from, "matrix")）强迫类的对象使用from类to，使用类所隐含的质量编码。当to是“矩阵”，所有的质量分数必须是相同的宽度，其结果是一个矩阵式integer。结果始终代表
narrow signature(x = "FastqQuality", start = NA, end = NA, width = NA, use.names = TRUE): "narrow" quality so that scores are between start and end bases, according to narrow in the IRanges
窄signature(x = "FastqQuality", start = NA, end = NA, width = NA, use.names = TRUE)：窄quality所以，分数之间start和end碱基，根据narrowIRanges
trimTailw signature(object="FastqQuality", 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="FastqQuality", 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="FastqQuality", k="integer", a="character", successive=FALSE, ..., ranges=FALSE): trim trailing scores if k scores fall below the quality encoded by a. If successive=FALSE, the k'th failing score and all subseqent scores are trimmed. If successive=TRUE, failing scores must occur successively; the sequence is trimmed
trimTailssignature(object="FastqQuality", k="integer", a="character", successive=FALSE, ..., ranges=FALSE)：修剪尾随分数如果k分数低于a编码的质量下降。如果successive=FALSE，被修剪的第k个未能得分和所有subseqent分数。如果successive=TRUE，未能得分必须先后发生顺序修剪
srorder signature(x = "FastqQuality"):
srordersignature(x = "FastqQuality")：
srrank signature(x = "FastqQuality"):
srranksignature(x = "FastqQuality")：
srduplicated signature(x = "FastqQuality"):
srduplicatedsignature(x = "FastqQuality")：
Apply srsort, srorder, srrank, and srduplicated to quality scores, returning objects as
应用srsort，srorder，srrank，srduplicated质量分数，返回对象
Integer representations of SFastqQuality and FastqQuality can be obtained with as(x, "matrix").
SFastqQuality和FastqQuality可以用as(x, "matrix")得到的整数表示。
作者（S）----------Author(s)----------
Martin Morgan <mtmorgan@fhcrc.org>
参见----------See Also----------
NumericQuality and other constructors.
NumericQuality和其他构造。
举例----------Examples----------
names(slot(getClass("QualityScore"), "subclasses"))
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 14:05:08
