RLEBindScore-class(ChIPseqR)
RLEBindScore-class()所属R语言包：ChIPseqR
Run-length Encoded Binding Site Scores
运行长度编码的结合位点得分
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class provides a memory efficient representation of binding site scores.
这个类提供了内存效率的结合位点的分数表示。
类的对象----------Objects from the Class----------
Objects can be created by calls of the form BindScore(functionCall, score, pvalue, peaks, cutoff, nullDist, names, start, digits, compress=TRUE) or through calls to callBindingSites.
对象可以创建形式BindScore(functionCall, score, pvalue, peaks, cutoff, nullDist, names, start, digits, compress=TRUE)检测或通过调用callBindingSites。
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 run-length encoded numeric vector per chromosome.
score类"list"的对象。结合现场评分。一个运行长度编码，每个染色体的数字向量。
pvalue: Object of class "list". The (adjusted and run-length encoded) p-values corresponding to the scores in slot score.
pvalue类"list"的对象。 （调整后的运行长度编码）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）。
延伸----------Extends----------
Class "BindScore", directly.
类"BindScore"，直接。
方法----------Methods----------
decompress signature(x = "RLEBindScore"): conversion to BindScore object.
解压缩signature(x = "RLEBindScore")：BindScore对象的转换。
作者（S）----------Author(s)----------
Peter Humburg
参见----------See Also----------
BindScore, Rle
BindScore，Rle
举例----------Examples----------
showClass("RLEBindScore")
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=TRUE)
## 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 14:53:21
