BindScore-class(ChIPseqR)
BindScore-class()所属R语言包：ChIPseqR
Class "BindScore"
类“BindScore”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class provides the infrastructure to store results of ChIP-seq analysis.
这个类提供了基础设施，存储芯片SEQ分析的结果。
用法----------Usage----------
## S4 method for signature 'BindScore'
binding(x)
## S4 method for signature 'BindScore'
chrLength(x, subset)
## S4 method for signature 'BindScore'
cutoff(x, type=c("score", "pvalue"))
## S4 replacement method for signature 'BindScore'
cutoff(x, type=c("score", "pvalue")) <- value
## S4 method for signature 'BindScore'
head(x, n=6, by=c("score", "position"), ...)
## S4 method for signature 'BindScore'
lapply(X, FUN, ...)
## S4 method for signature 'BindScore'
length(x)
## S4 replacement method for signature 'BindScore'
length(x) <- value
## S4 method for signature 'BindScore'
max(x, ..., na.rm=TRUE)
## S4 method for signature 'BindScore'
min(x, ..., na.rm=TRUE)
## S4 method for signature 'BindScore'
names(x)
## S4 replacement method for signature 'BindScore,ANY'
names(x) <- value
## S4 method for signature 'BindScore'
nullDist(x)
## S4 replacement method for signature 'BindScore'
nullDist(x) <- value
## S4 method for signature 'BindScore'
peaks(x, ...)
## S4 method for signature 'BindScore'
range(x, ..., na.rm=TRUE)
## S4 method for signature 'BindScore'
score(x)
## S4 method for signature 'BindScore'
support(x)
## S4 method for signature 'BindScore'
tail(x, n=6, by=c("score", "position"), ...)
BindScore(call, score=list(), pvalue=list(), peaks=list(), cutoff=c(-Inf, 1), nullDist=c(0, 1), names=NULL, start=1L, compress=TRUE, digits=16)
参数----------Arguments----------
参数：x
Object of class BindScore.
对象类BindScore。
参数：X
Object of class BindScore.
对象类BindScore。
参数：subset
Index vector indicating a subset of x. If subset is missing everything is selected.
索引向量表明了x子集。如果subset缺少一切都被选中。
参数：type
A string indicating which type of cut-off should be returned or changed. Either "score" or "pvalue"
一个字符串，指示应退还或更改截止类型。要么"score"或"pvalue"
参数：n
Number of entries to show.
显示的条目数。
参数：by
A string indicating whether the output should be sorted by score or by position in the genome.
一个字符串，指示输出是否应得分或由基因组中的位置排序。
参数：na.rm
Logical indication whether NAs should be ignored.
逻辑指示是否NAs应该被忽略。
参数：FUN
Function to apply to results for each chromosome.
功能适用于每一个染色体的结果。
参数：value
Replacement value.
重置价值。
参数：call
Function call used to generate the values of the other slots.
函数调用中使用产生的其他插槽的值。
参数：score
List of binding site scores. One component per chromosome.
名单的结合位点的分数。每个染色体的一个组成部分。
参数：pvalue
List of binding site p-values. One component per chromosome.
结合位点的p值列表。每个染色体的一个组成部分。
参数：peaks
List of significant peaks in binding site score. One component per chromosome.
名单中的结合位点得分有显着的峰值。每个染色体的一个组成部分。
参数：cutoff
Numeric vector of length two indicating the significance cut-off in terms of score and p-value.
长度为二的数字矢量表明切断得分和p值的意义。
参数：nullDist
Parameters of the null distribution.
空分布的参数。
参数：names
Character vector providing names for chromosomes.
特征向量为染色体提供的名称。
参数：start
Integer indicating position of first binding site score.
整数，指示位置的第一份具有约束力的网站评分。
参数：compress
Logical indicating whether scores and p-values should be compressed.
逻辑说明得分和p值是否应压缩。
参数：digits
The number of decimal places to retain for compression.
小数点后保留压缩。
参数：...
Further arguments.
进一步的论据。
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("BindScore", functionCall, score, pvalue, peaks, cutoff, nullDist, names, ...). Objects of this class are typically created (and returned) by functions that perform peak calling on ChIP-seq data. Usually there should be no need to create them directly.
创建对象可以通过检测的形式new("BindScore", functionCall, score, pvalue, peaks, cutoff, nullDist, names, ...)。通常是创建这个类的对象（返回）执行对芯片SEQ数据高峰通话功能。一般应该是有没有必要建立直接。
插槽----------Slots----------
functionCall: Object of class "call" storing the function call used to initiate the analysis.
functionCall类"call"存储功能的对象调用用于启动的分析。
score: Object of class "list". The binding site score. One numeric vector per chromosome.
score类"list"的对象。结合现场评分。每一个数字矢量染色体。
pvalue: Object of class "list". The (adjusted) p-values corresponding to the scores in slot score.
pvalue类"list"的对象。 （调整）的P-值对应插槽score分数。
peaks: Object of class "list" giving the location of significant peaks in the binding site score. These correspond to the location of predicted binding sites.
peaks：Object类的"list"结合位点得分显着峰的位置。这些对应于预测的结合位点的位置。
cutoff: Object of class "numeric" with entries "pvalue" and "score" giving the significance threshold used for peak calling in terms of p-value and score.
cutoff：Object类的"numeric"条目pvalue“和”得分“赋予的意义阈值，p值和得分调用高峰的。
nullDist: Object of class "numeric" providing the parameters of the null distribution used to determine p-values.
nullDist类"numeric"提供空分布的参数，用来确定p值的对象。
start: Object of class "integer" indicating the index corresponding to the first entry in score (assumed to be the same for all chromosomes).
start：Object类的"integer"表示相应的第一项指标score（假设是所有染色体的相同）。
方法----------Methods----------
as.data.frame signature(x = "BindScore"): Convert results into a data.frame giving the location, score and p-value of significant peaks.
as.data.framesignature(x = "BindScore")：data.frame位置，得分和p值的重大峰转换成结果。
[ signature(x = "BindScore", i = "ANY", j = "missing", drop = "missing"): Restrict results to a subset of chromosomes. Chromosomes can either be identified by name or by numerical index.
[signature(x = "BindScore", i = "ANY", j = "missing", drop = "missing")：限制结果染色体的一个子集。染色体可以通过名称或索引数值确定。
[[ signature(x = "BindScore", i = "ANY", j = "missing"): Restrict results to a single chromosome. Note that x[["chr1"]] is identical to x["chr1"].
[signature(x = "BindScore", i = "ANY", j = "missing")结果限制到一个单一的染色体。注意x[["chr1"]]是相同的x["chr1"]。
[[ signature(x = "BindScore", i = "ANY", j = "numeric"): subset results to restrict them to a region on a single chromosome.
[signature(x = "BindScore", i = "ANY", j = "numeric")：一条染色体上的区域限制他们的子集的结果。
binding signature(x = "BindScore"): Returns length of binding site used during analysis.
结合signature(x = "BindScore")：返回在分析过程中使用的结合位点的长度。
chrLength signature(x = "BindScore", subset = "ANY"): Returns length of all chromosomes represented in x.
chrLengthsignature(x = "BindScore", subset = "ANY")：返回长度代表x的所有染色体。
cutoff<- signature(x = "BindScore"): Sets the significance cut-off. Argument type=c("score", "pvalue") determines which cut-off is to be set, the other is adjusted accordingly. This recalculates the significance of peaks in the binding site score and may be slow.
截止< - signature(x = "BindScore")：设置切断的意义。参数type=c("score", "pvalue")决定切断要设置的，其他相应的调整。这将重新计算结合现场评分峰的意义，并可能会很慢。
cutoff signature(x = "BindScore"): Returns significance threshold used for analysis.
截止signature(x = "BindScore")：返回意义阈值用于分析。
head signature(x = "BindScore"): Returns the first n peaks. Argument by = c("score", "position") determines whether results are sorted by score or by genomic location.
头signature(x = "BindScore")：返回第一n峰。参数by = c("score", "position")决定是否得分或由基因组的位置排序结果。
lapply signature(X = "BindScore"): Applies a function to results for each chromosome.
lapplysignature(X = "BindScore")：应用功能，每个染色体的结果。
length<- signature(x = "BindScore"): Reduces the number of chromosomes for which results are stored, i.e., length(x) <- 3 only retains the first three chromosomes.
长度< - signature(x = "BindScore")：降低存储结果的染色体数目，即length(x) <- 3只保留前三个染色体。
length signature(x = "BindScore"): Returns the number of binding sites identified by the analysis.
长度signature(x = "BindScore")：返回分析所确定的结合位点的数目。
max signature(x = "BindScore"): Returns maximum score.
最大signature(x = "BindScore")：返回最高得分。
min signature(x = "BindScore"): Returns minimum score.
分signature(x = "BindScore")：返回的最低分数。
names<- signature(x = "BindScore", value = "ANY"): Sets the chromosome names.
名称< - signature(x = "BindScore", value = "ANY")：设置染色体的名字。
names signature(x = "BindScore"): Returns the chromosome names.
名称signature(x = "BindScore")：返回染色体的名称。
nullDist<- signature(x = "BindScore"): Sets the parameters of the null distribution adjusting the significance cut-off in the process and predicts binding sites using the new null distribution.
nullDist < - signature(x = "BindScore")：设置调整的意义，在这个过程中切断空分布的参数，并预测使用新的空分布的结合位点。
peaks signature(x = "BindScore"): Returns list of predicted binding sites.
峰signature(x = "BindScore")：返回列表预测的结合位点。
range signature(x = "BindScore"): Range of binding site scores.
范围signature(x = "BindScore")：结合位点的分数范围。
score signature(x = "BindScore"): Returns list of binding site scores.
得分signature(x = "BindScore")：返回列表的结合位点的分数。
support signature(x = "BindScore"): Returns length of support region used during analysis.
支持signature(x = "BindScore")：返回支持区域的长度，在分析过程中使用。
tail signature(x = "BindScore"): Returns the last n peaks. Argument by = c("score", "position") determines whether results are sorted by score or by genomic location.
尾巴signature(x = "BindScore")：返回最后n峰。参数by = c("score", "position")决定是否得分或由基因组的位置排序结果。
作者（S）----------Author(s)----------
Peter Humburg
参考文献----------References----------
<h3>See Also</h3> <code>ReadCounts</code> for the data structure used as input for the analysis and <code>callBindingSites</code>
举例----------Examples----------
showClass("BindScore")
set.seed(1)
## determine binding site locations[＃确定有约束力的地点。]
b <- sample(1:1e6, 5000)
## sample read locations[＃示例读取位置]
fwd <- unlist(lapply(b, function(x) sample((x-83) x-73), 20, replace=TRUE)))
rev <- unlist(lapply(b, function(x) sample((x+73)x+83), 20, replace=TRUE)))
## add some background noise[＃添加一些背景噪音。]
fwd <- c(fwd, sample(11e6-25), 50000))
rev <- c(rev, sample(25:1e6, 50000))
## create data.frame with read positions as input to strandPileup[＃创建一个数据框读输入到strandPileup的位置]
reads <- data.frame(chromosome="chr1", position=c(fwd, rev),
length=25, strand=factor(rep(c("+", "-"), times=c(150000, 150000))))
## create object of class ReadCounts[＃创建对象类ReadCounts]
readPile <- strandPileup(reads, chrLen=1e6, extend=1, plot=FALSE)
## predict binding site locations[＃预测约束力的地点。]
## the artificial dataset is very small so predictions may not be very reliable[＃人工数据集非常小，这样的预测可能不是很可靠]
bindScore <- simpleNucCall(readPile, bind=147, support=20, plot=FALSE, compress=FALSE)
## number of binding sites found[＃结合位点发现]
length(bindScore)
## the first few predictions, by score[＃最初的几个预测，得分]
head(bindScore)
## score and p-value cut-off used[＃得分和p值，使用截止]
cutoff(bindScore)
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。
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发表于 2012-2-25 14:51:06
