PileupParam(Rsamtools)
PileupParam()所属R语言包：Rsamtools
Parameters for creating pileups from BAM files
参数为创建的BAM文件pileups
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Use PileupParam() to create a parameter object influencing what fields and which records are used to calculate pile-ups, and to influence the values returned.
使用PileupParam()创建一个参数对象，对哪些领域和哪些记录被用来计算桩，并影响返回的值。
用法----------Usage----------
# Constructor
PileupParam(flag = scanBamFlag(),
minBaseQuality = 13L, minMapQuality = 0L,
minDepth = 0L, maxDepth = 250L,
yieldSize = 1L, yieldBy = c("range", "position"), yieldAll = FALSE,
which = GRanges(), what = c("seq", "qual"))
# Accessors
plpFlag(object)
plpFlag(object) <- value
plpMaxDepth(object)
plpMaxDepth(object) <- value
plpMinBaseQuality(object)
plpMinBaseQuality(object) <- value
plpMinDepth(object)
plpMinDepth(object) <- value
plpMinMapQuality(object)
plpMinMapQuality(object) <- value
plpWhat(object)
plpWhat(object) <- value
plpWhich(object)
plpWhich(object) <- value
plpYieldAll(object)
plpYieldAll(object) <- value
plpYieldBy(object)
plpYieldBy(object) <- value
plpYieldSize(object)
plpYieldSize(object) <- value
## S4 method for signature 'PileupParam'
show(object)
参数----------Arguments----------
参数：flag
An instance of the object returned by scanBamFlag, restricting various aspects of reads to be included or excluded.
scanBamFlag返回一个对象的实例，限制各个方面的内容要包含或排除。
参数：minBaseQuality
The minimum read base quality below which the base is ignored when summarizing pileup information.
最低的阅读碱基质量低于该碱基总结堆积的信息时，被忽略。
参数：minMapQuality
The minimum mapping quality below which the entire read is ignored.
最低映射质量低于整个读取被忽略。
参数：minDepth
The minimum depth of the pile-up below which the position is ignored.
桩的最小深度低于该位置将被忽略。
参数：maxDepth
The maximum depth of reads considered at any position; this can be used to limit memory consumption.
认为在任何位置读取的最大深度，这可以用来限制内存消耗。
参数：yieldSize
The number of records to include in each call to FUN.
记录的数量，包括在每个调用FUN。
参数：yieldBy
How records are to be counted. By range (in which case yieldSize must equal 1) means that FUN is invoked once for each range in which. By position means that FUN is invoked whenever pile-ups have been accumulated for yieldSize positions, regardless of ranges in which.
记录是如何计算的。由范围（在这种情况下，yieldSize必须等于1）意味着，FUN调用每个范围的一次which。由地位意味着FUN被调用时，桩已累计yieldSize阵地，无论在which不等。
参数：yieldAll
Whether to report all positions (yieldAll=TRUE), or just those passing the filtering criteria of flag, minBaseQuality, etc. When yieldAll=TRUE, positions not passing filter criteria have "0" entries in seq or qual.
是否所有职位（yieldAll=TRUE），或只是路过flag，minBaseQuality等yieldAll=TRUE，职位不及格筛选条件的筛选条件“ seq或qual0条目。
参数：which
A GRanges or RangesList instance restricting pileup calculations to the corresponding genomic locations.
一个GRanges或RangesList例如限制堆积计算相应的基因的位置。
参数：what
A character() instance indicating what values are to be returned. One or more of c("seq", "qual").
一个character()实例说明什么样的价值观是要返回。一个或多个的c("seq", "qual")。
参数：object
An instace of class PileupParam.
一个类PileupParaminstace。
参数：value
An instance to be assigned to the corresponding slot of the PileupParam instance.
被分配到相应的插槽PileupParam实例，一个实例。
类的对象----------Objects from the Class----------
Objects are created by calls of the form PileupParam().
对象的创建形式PileupParam()检测。
插槽----------Slots----------
Slot interpretation is as described in the "Arguments" section.
槽的解释“参数”部分中所述。
flag Object of class integer encoding flags to be kept when they have their '0' (keep0) or '1'
flag类integer编码保存的标志时，他们有他们0对象（keep0）或1
minBaseQuality An integer(1).
minBaseQualityinteger(1)。
minMapQuality An integer(1).
minMapQualityinteger(1)。
minDepth An integer(1).
minDepthinteger(1)。
maxDepth An integer(1).
maxDepthinteger(1)。
yieldSize An integer(1).
yieldSizeinteger(1)。
yieldBy An character(1).
yieldBycharacter(1)。
yieldAll A logical(1).
yieldAllAlogical(1)。
which A GRanges or RangesList instance.
whichAGRanges或RangesList实例。
what A character().
whatAcharacter()。
函数和方法----------Functions and methods----------
See 'Usage' for details on invocation.
在调用的详细信息，请参阅“用法”。
Constructor:
构造：
PileupParam: Returns a PileupParam object.
PileupParam：返回PileupParam对象。
Accessors: get or set corresponding slot values; for setters, value is coerced to the type of the corresponding slot.
存取：获取或设置相应的槽值的制定者，value裹挟到相应的插槽类型。
plpFlag, plpFlag<- Returns or sets the named integer
plpFlag，plpFlag < - 返回或设置名为integer
plpMinBaseQuality, plpMinBaseQuality<- Returns or sets an
plpMinBaseQuality，plpMinBaseQuality < - 返回或设置一个
plpMinMapQuality, plpMinMapQuality<- Returns or sets an
plpMinMapQuality“，plpMinMapQuality < - 返回或设置
plpMinDepth, plpMinDepth<- Returns or sets an
plpMinDepth，plpMinDepth < - 返回或设置一个
plpMaxDepth, plpMaxDepth<- Returns or sets an integer(1) vector of the maximum depth to which pileups are
plpMaxDepth，plpMaxDepth < - 返回或设置向量的最大深度，这pileups integer(1)
plpYieldSize, plpYieldSize<- Returns or sets an
plpYieldSize，plpYieldSize < - 返回或设置一个
plpYieldBy, plpYieldBy<- Returns or sets an character(1) vector determining how pileups will be
plpYieldBy，plpYieldBy < - 返回或设置一个character(1)向量确定如何pileups会
plpYieldAll, plpYieldAll<- Returns or sets an logical(1) vector indicating whether all positions, or just
plpYieldAll，plpYieldAll < - 返回或设置logical(1)向量表示，是否所有职位，或者只是
plpWhich, plpWhich<- Returns or sets the object influencing
plpWhich，plpWhich < - 返回或设置对象的影响
plpWhat, plpWhat<- Returns or sets the character
plpWhat，plpWhat < - 返回或设置了character
Methods:
方法：
show Compactly display the object.
显示紧显示对象。
作者（S）----------Author(s)----------
Martin Morgan
参见----------See Also----------
applyPileups.
applyPileups。
举例----------Examples----------
example(applyPileups)
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。
|
发表于 2012-2-26 13:29:13
