AlignedRead-class(ShortRead)
AlignedRead-class()所属R语言包：ShortRead
"AlignedRead" class for aligned short reads
对齐短读“AlignedRead”类
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class represents and manipulates reads and their genomic alignments. Alignment information includes genomic position, strand, quality, and other data.
这个类代表和操纵读取和他们的基因组比对。对齐信息，包括基因组的位置，钢绞线，质量，和其他数据。
类的对象----------Objects from the Class----------
Objects of this class can be created from a call to the AlignedRead constructor, or more typically by parsing appropriate files (e.g., readAligned).
可以创建这个类的对象调用的AlignedRead构造，或更通常解析相应的文件（例如，readAligned）。
插槽----------Slots----------
chromosome Object of class "factor" the particular sequence within a set of target sequences (e.g. chromosomes in a genome assembly) to which each short read
chromosome类"factor"一组靶序列（如染色体在基因组组装）内特定序列的对象，每个短读
position Object of class "integer" the (base-pair) position in the genome to which the read is aligned. AlignedRead objects created by readAligned use 1-based indexing, with alignemnts reported in "left-most"
positionObject类的"integer"（碱基对）的位置在它的基因组读对齐。 AlignedRead由readAligned使用基于1的索引创建的对象，在最左边的“报告alignemnts
strand Object of class "factor" the strand of
strand类"factor"钢绞线的对象
alignQuality Object of class "numeric"
alignQualityObject类的"numeric"
alignData Object of class "AlignedDataFrame"
alignDataObject类的"AlignedDataFrame"
quality Object of class "BStringSet"
qualityObject类的"BStringSet"
sread Object of class "DNAStringSet" DNA
sread类"DNAStringSet"的DNA的对象
id Object of class "BStringSet" read
idObject类的"BStringSet"读
延伸----------Extends----------
Class "ShortReadQ", directly. Class "ShortRead", by class "ShortReadQ", distance 2. Class ".ShortReadBase", by class "ShortReadQ", distance 3.
类"ShortReadQ"，直接。类"ShortRead"，类“ShortReadQ”，距离为2。类".ShortReadBase"，类“ShortReadQ”，距离3。
方法----------Methods----------
See accessors for additional functions to access slot content, and ShortReadQ, ShortRead for inherited methods. Additional methods include:
看到accessors附加功能访问插槽含量，ShortReadQ，ShortRead继承的方法。其他方法包括：
[ signature(x = "AlignedRead", i = "ANY", j = "missing"): This method creates a new AlignedRead object containing only those reads indexed by i. chromosome is recoded to
[signature(x = "AlignedRead", i = "ANY", j = "missing")：此方法创建一个新的AlignedRead对象，其中包含只有那些索引读取i。 chromosome被重新编码
append signature(x = "AlignedRead", values = "AlignedRead", length = "missing"): append values after x. chromosome and strand must be factors with the same levels. See methods for ShortReadQ, AlignedDataFrame for details of how
追加signature(x = "AlignedRead", values = "AlignedRead", length = "missing")：追加values后x。 chromosome和strand必须具有相同水平的因素。如何的详细信息，请参阅ShortReadQ，AlignedDataFrame方法
signature(from = "PairwiseAlignedXStringSet", to = "AlignedRead"):
signature(from = "PairwiseAlignedXStringSet", to = "AlignedRead")：
signature(from = "AlignedRead", to = "RangesList"): signature(from = "AlignedRead", to = "RangedData"): signature(from = "AlignedRead", to = "GRanges"): signature(from = "AlignedRead", to = "GappedAlignments"): signature(from = "AlignedRead", to = "GappedReads"):
signature(from = "AlignedRead", to = "RangesList")：signature(from = "AlignedRead", to = "RangedData")：signature(from = "AlignedRead", to = "GRanges")：signature(from = "AlignedRead", to = "GappedAlignments")：signature(from = "AlignedRead", to = "GappedReads")：
Invoke these methods with, e.g., as(from, "AlignedRead") to coerce objects of class from to class "AlignedRead".
调用这些方法，例如as(from, "AlignedRead")强迫的from类"AlignedRead"类对象。
Coercion from AlignedRead to RangesList, RangedData or GRanges assumes that position(from) uses a "leftmost" (see coverage on this page) coordinate system. Since Ranges objects cannot store NA values, reads with NA in the position, width, chromosome or (in the case of GRanges) strand vectors are dropped.
胁迫，从AlignedRead RangesList，RangedData或农庄假定position(from)使用了“最左边的”（见coverage此页）坐标系统。由于范围对象不能存储NA值，读取用NAposition，width，chromosome（在农庄的情况下）strand 向量下跌。
chromosome signature(object = "AlignedRead"): access the
染色体signature(object = "AlignedRead")：访问
position signature(object = "AlignedRead"): access the
位置signature(object = "AlignedRead")：访问
strand signature(object = "AlignedRead"): access the
链signature(object = "AlignedRead")：访问
signature(x = "AlignedRead", shift = 0L, width = NULL, weight = 1L, ..., coords = c("leftmost", "fiveprime"), extend=0L):
signature(x = "AlignedRead", shift = 0L, width = NULL, weight = 1L, ..., coords = c("leftmost", "fiveprime"), extend=0L)：
Calculate coverage across reads present in x.
计算覆盖率跨读取x。
shift must be either 0L or a named integer vector with names including all levels(chromosome(x)). It specifies how the reads in x should be (horizontally) shifted before the coverage is computed.
shift必须要么0L或命名的名称，包括所有的levels(chromosome(x))整数向量。它指定如何在x应该是（水平）转移前的覆盖率计算读取。
width must be either NULL or a named vector of non-negative integers with names including all levels(chromosome(x)). In the latter case, it specifies for each chromosome the end of the chromosome region over which coverage is to be calculated after the reads have been shifted. Note that this region always starts at chromosome position 1. If width is NULL, it ends at the rightmost chromosome position covered by at least one read.
width必须是NULL或命名的名称，包括所有的levels(chromosome(x))向量的非负整数。在后一种情况下，它指定为每个染色体的染色体区域覆盖计算后读取已转移结束。请注意，该区域一直在1号染色体的位置开始。如果width是NULL，它包括至少一个只读的位置在最右边的染色体结束。
weight must be 1L for now (weighting the reads is not supported yet, sorry).
weight必须1L现在（加权读取不支持，对不起）。
coords specifies the coordinate system used to record position. Both systems number base pairs from left to right on the 5' strand. leftmost indicates the eland convention, where position(x) is the left-most (minimum) base pair, regardless of strand. fiveprime is the MAQ convention, where position(x) is the coordinate of the 5' end of the aligned read.
coords指定用来记录位置的坐标系。这两个系统从左至右数个碱基对上的5链。 leftmost表示羚羊的公约，其中position(x)（最小）是最左边的碱基对，不管链。 fiveprime是MAQ公约，其中position(x)是对齐的读的5端的坐标。
extend indicates the number of base pairs to extend the read. Extension is in the 3' direction, measured from the 3' end of the aligned read.
extend表示碱基对的数量，延长读。扩展是在3的方向测量，从3结束的对齐的读。
The return value of coverage is a SimpleRleList object.
返回值的coverageSimpleRleList对象。
signature(x = "AlignedRead", table = "RangesList"):
signature(x = "AlignedRead", table = "RangesList")：
Return a length(x) logical vector indicating whether the chromosome, position, and width of x overlap (see IRanges overlap) with ranges in table. Reads for which chromosome(), position(), or width() return NA never overlap with table. This function assumes that positions are in "leftmost" coordinates, as defined in coverage.
返回一个长度（X）逻辑向量，说明是否染色体，位置和x重叠的宽度（见IRangesoverlap）table的范围。为读取chromosome()，position()或width()回NA从来没有用table重叠。这个函数假设的立场是“最左边的坐标，定义在coverage。
srorder signature(x = "AlignedRead", ..., withSread=TRUE):
srordersignature(x = "AlignedRead", ..., withSread=TRUE)：
srrank signature(x = "AlignedRead", ..., withSread=TRUE):
srranksignature(x = "AlignedRead", ..., withSread=TRUE)：
srsort signature(x = "AlignedRead", ..., withSread=TRUE):
srsortsignature(x = "AlignedRead", ..., withSread=TRUE)：
srduplicated signature(x = "AlignedRead", ..., withSread=TRUE):
srduplicatedsignature(x = "AlignedRead", ..., withSread=TRUE)：
Order, rank, sort, and find duplicates in AlignedRead objects. Reads are sorted by chromosome, strand, position, and then (if withSread=TRUE) sread; less fine-grained sorting can be accomplished with, e.g., x[srorder(sread(x))]. srduplicated behaves like duplicated, i.e., the first copy of a duplicate is
订单，排名，排序，发现在AlignedRead对象的重复。读取排序chromosome，strand，position，然后（如果withSread=TRUE）sread;减细粒度的排序，例如可以完成， x[srorder(sread(x))]。 srduplicatedduplicated，即行为的，重复的第一个副本
show signature(object = "AlignedRead"): provide a
显示signature(object = "AlignedRead")：提供1
detail signature(x = "AlignedRead"): display
详细signature(x = "AlignedRead")：显示
作者（S）----------Author(s)----------
Martin Morgan <mtmorgan@fhcrc.org>
参见----------See Also----------
readAligned
readAligned
举例----------Examples----------
showMethods(class="AlignedRead", where=getNamespace("ShortRead"))
dirPath <- system.file('extdata', 'maq', package='ShortRead')
(aln <- readAligned(dirPath, 'out.aln.1.txt', type="MAQMapview"))
coverage(aln)[[1]]
cvg <- coverage(aln, shift=c(ChrA=10L))
## remove 0 coverage on left ends[＃删除0左两端覆盖]
ltrim0 <- function(x) {
i <- !cumprod(runValue(x) == 0)
Rle(runValue(x)[i], runLength(x)[i])
}
endoapply(cvg, ltrim0)
## demonstration of show() and detail() methods[＃show（）和详细（）方法示范]
show(aln)
detail(aln)
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。
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发表于 2012-2-26 14:03:00
