ShortRead-class(ShortRead)
ShortRead-class()所属R语言包：ShortRead
"ShortRead" class for short reads
“ShortRead”类短期读取
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, uniform-length short reads and their identifiers.
这个类提供了一种协调的方式，统一短读取和自己的标识符，存储和操纵。
类的对象----------Objects from the Class----------
Objects from this class are created by readFasta, or by calls to the constructor ShortRead, as outlined below.
从这个类的对象被创建readFasta，或调用的构造ShortRead，概述如下。
插槽----------Slots----------
sread: Object of class "DNAStringSet" containing IUPAC-standard, uniform-length DNA strings represent
sread类"DNAStringSet"含有的IUPAC标准，统一长度的DNA字符串对象代表
id: Object of class "BStringSet" containing
id：Object类的"BStringSet"包含
延伸----------Extends----------
Class ".ShortReadBase", directly.
类".ShortReadBase"，直接。
方法----------Methods----------
Constructors include:
构造包括：
ShortRead signature(sread = "DNAStringSet", id = "BStringSet"): Create a ShortRead object from reads and their
ShortReadsignature(sread = "DNAStringSet", id = "BStringSet")：从读中创建一个ShortRead对象及其
ShortRead signature(sread = "DNAStringSet", id = "missing"):
ShortReadsignature(sread = "DNAStringSet", id = "missing")：
ShortRead signature(sread = "missing", id = "missing", ...):
ShortReadsignature(sread = "missing", id = "missing", ...)：
Methods include:
方法包括：
sread signature(object = "AlignedRead"): access the
SREADsignature(object = "AlignedRead")：访问
id signature(object = "AlignedRead"): access the
IDsignature(object = "AlignedRead")：访问
[ signature(x = "ShortRead", i = "ANY", j = "missing"): This method creates a new ShortRead object containing only those reads indexed by i. Additional methods on "[,ShortRead" do not provide additional functionality, but
[signature(x = "ShortRead", i = "ANY", j = "missing")：此方法创建一个新的ShortRead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 = "ShortRead", values = "ShortRead", length = "missing"): append the sread and id slots of values after
追加signature(x = "ShortRead", values = "ShortRead", length = "missing")：sread和idvalues后槽追加
narrow signature(x = "ShortRead", start = NA, end = NA, width = NA, use.names = TRUE): "narrow" sread so that sequences are between start and end bases, according to narrow in the IRanges package.
窄signature(x = "ShortRead", start = NA, end = NA, width = NA, use.names = TRUE)：窄sread使序列之间start和end碱基，根据narrowIRanges包。
length signature(x = "ShortRead"): returns a integer(1) vector describing the number of reads in this
长度signature(x = "ShortRead")：返回integer(1)矢量描述，在此读取
width signature(x = "ShortRead"): returns an integer() vector of the widths of each read in this
宽度signature(x = "ShortRead")：返回integer()每次读取的宽度向量，
srorder signature(x = "ShortRead"):
srordersignature(x = "ShortRead")：
srrank signature(x = "ShortRead"):
srranksignature(x = "ShortRead")：
srsort signature(x = "ShortRead"):
srsortsignature(x = "ShortRead")：
srduplicated signature(x = "ShortRead"): Order, rank, sort, and find duplicates in ShortRead objects based on sread(x), analogous to the corresponding functions order, rank, sort, and duplicated,
srduplicatedsignature(x = "ShortRead")：订单，排名，排序，查找重复ShortRead上sread(x)的对象，相应的功能类似于order，rank，sort，duplicated
srdistance signature(pattern="ShortRead", subject="ANY"): Find the edit distance between each read in pattern and the (short) sequences in subject. See srdistance for allowable values for subject, and for additional
srdistancesignature(pattern="ShortRead", subject="ANY")：查找pattern和subject（短）序列的每个读之间的编辑距离。看到srdistancesubject的允许值，并额外
trimLRPatterns signature(Lpattern = "", Rpattern = "", subject = "ShortRead", max.Lmismatch = 0, max.Rmismatch = 0, with.Lindels = FALSE, with.Rindels = FALSE, Lfixed = TRUE, Rfixed = TRUE, ranges = FALSE):
trimLRPatternssignature(Lpattern = "", Rpattern = "", subject = "ShortRead", max.Lmismatch = 0, max.Rmismatch = 0, with.Lindels = FALSE, with.Rindels = FALSE, Lfixed = TRUE, Rfixed = TRUE, ranges = FALSE)：
Remove left and / or right flanking patterns from sread(subject), as described in trimLRPatterns. Classes derived from ShortRead (e.g., ShortReadQ, AlignedRead) have corresponding base quality scores trimmed, too. The class of the return object is the same as the class of subject, except when ranges=TRUE when the
删除左和/或右sread(subject)trimLRPatterns，从侧翼模式。来自类ShortRead（例如，ShortReadQ，AlignedRead）有相应的基础质量分数修剪，太。返回对象的类是作为类subject相同，除非ranges=TRUE时
alphabetByCycle signature(stringSet = "ShortRead"): Apply alphabetByCycle to the sread component of stringSet, returning a matrix as described in
alphabetByCyclesignature(stringSet = "ShortRead")：申请alphabetByCyclesread组件stringSet，返回一个矩阵中所述
tables signature(x= "ShortRead", n = 50): Apply tables to the sread component of x, returning a list summarizing frequency of reads in
表signature(x= "ShortRead", n = 50)：申请tables组件sread返回列表总结频率读取x
clean signature(object="ShortRead"): Remove all reads
洁净signature(object="ShortRead")：删除所有的读取
show signature(object = "ShortRead"): provides a brief
显示signature(object = "ShortRead")：提供了一个简短的
detail signature(x = "ShortRead"): provides a more extensive summary of this object, displaying the first and
详细signature(x = "ShortRead")：这个对象提供了一个更广泛的总结，显示第一和
writeFasta signature(object, file, ...): write object to file in fasta format. See
writeFastasignature(object, file, ...)：写objectfileFASTA格式。见
作者（S）----------Author(s)----------
Martin Morgan
参见----------See Also----------
ShortReadQ
ShortReadQ
举例----------Examples----------
showClass("ShortRead")
showMethods(class="ShortRead", where=getNamespace("ShortRead"))
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注：
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发表于 2012-2-26 14:07:31
