callBindingSites-methods(ChIPseqR)
callBindingSites-methods()所属R语言包：ChIPseqR
Predict protein binding sites from high-throughput sequencing data
从高通量测序数据预测蛋白质结合位点
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Methods for function callBindingSites in Package "ChIPseqR". These methods are used to identify protein binding sites from ChIP-seq data.
方法函数callBindingSites包ChIPseqR“。使用这些方法，以确定芯片SEQ数据从蛋白结合位点。
用法----------Usage----------
## S4 method for signature 'ANY'
callBindingSites(data, chrLen, plot=TRUE, verbose=TRUE, ..., plotTo)
## S4 method for signature 'character'
callBindingSites(data, type, minQual=70, ...)
## S4 method for signature 'matrix'
callBindingSites(data, chrName="chr", ...)
## S4 method for signature 'ReadCounts'
callBindingSites(data, bind, support, background, bgCutoff=0.9, supCutoff=0.9,
fdr = 0.05, extend=1, tailCut=0.95, piLambda=0.5, adapt=FALSE, corSummary=median, compress = TRUE,
digits = 16, plot=TRUE, verbose=TRUE, ask=FALSE, plotTo, ...)
参数----------Arguments----------
参数：data
Either an object containing information about mapped reads or a list. See below for details.
无论是一个对象，其中包含映射读取信息或列表。细节见下文。
参数：bind
Length of binding region to use (see Details).
结合区域使用的长度（见详情）。
参数：support
Length of support region to use (see Details).
支持区域使用的长度（见详情）。
参数：background
Length of background window. If this is missing it will be set to 10*(bind+2*support).
背景窗口的长度。如果缺少它会被设定为10 *（bind+2 *support）。
参数：chrLen
Numeric vector indicating the length of all chromosomes. Only needed when data is an AlignedRead object. readBfaToc may be used to supply this information.
数字矢量显示所有染色体的长度。只需data是AlignedRead对象。 readBfaToc可以用来提供这些信息。
参数：bgCutoff
Numeric value between 0.5 and 1. This determines how much estimates of the background read density are allowed to vary for adjacent windows. Set to 1 to disable cutoff.
0.5和1之间的数值。这就决定允许多少背景读取密度估计因相邻窗口。设置为1，禁用截止。
参数：supCutoff
Numeric value between 0.5 and 1. This determines how much estimates of the support region read density are allowed to vary for forward and reverse strand. Set to 1 to disable cutoff.
0.5和1之间的数值。这就决定了多少支持区域估计读取密度允许不同的正向和反向链。设置为1，禁用截止。
参数：fdr
Target false discovery rate.
目标虚假的发现率。
参数：extend
Numeric value indicating how far mapped reads should be extended when calculating read counts.
数值表明多远映射读取应延长计算只读数时。
参数：type
Format of alignment file (see readAligned forr details).
对齐文件的格式（见readAlignedFORR细节）。
参数：minQual
Minimum alignment quality to use. All reads with lower alignment quality are discarded.
使用最小对齐质量。读取对齐质量较低的被丢弃。
参数：tailCut
Truncation point used to exclude outliers when estimating null distribution.
截断点用来排除离群值时，估计空分布。
参数：chrName
Name to use for the single chromosome.
要使用的名称为单条染色体。
参数：piLambda
If adapt=TRUE this parameter is used to estimate the proportion of scores not related to binding sites.
如果adapt=TRUE这个参数是用来估计不相关的结合位点的分数比例。
参数：adapt
Logical indicating whether an adaptive false discovery rate should be used. If this is FALSE (the default) the usual Benjamini-Hochberg procedure is used to control the FDR.
逻辑指示是否应使用一个自适应的错误发现率。如果这是FALSE（默认）通常Benjamini Hochberg过程控制FDR。
参数：corSummary
Function used to summarise cross-correlation across chromosomes. See the Details section on binding and support region.
总结整个染色体互相关函数中使用。请参阅上的约束力和支持区域的详细信息部分。
参数：compress
Logical indicating whether the return value should be compressed.
逻辑表示返回值是否应该被压缩。
参数：digits
Number of decimal places to retain for binding site score for compression.
数小数点后保留压缩结合现场评分。
参数：plot
Logical. If plot=TRUE (the default) some diagnostic plots are produced during the analysis.
逻辑。如果plot=TRUE（默认）一些诊断图的分析过程中产生的。
参数：verbose
Logical. If verbose=TRUE (the default) status messages are printed to indicate progress.
逻辑。如果verbose=TRUE（默认）状态讯息打印来显示进度。
参数：ask
Logical. Setting this to TRUE causes the system to wait for user input before displaying a new plot. See devAskNewPage.
逻辑。此设置TRUE导致系统等待用户输入，然后显示一个新的图。看到devAskNewPage。
参数：plotTo
Character string giving the name of a file that should be used to store plots generated during the analysis. If this is not missing a pdf file with the given name will be created.
字符串给一个文件存储在分析过程中产生的图，应使用的名称。如果这不是缺少一个给定名称的PDF文件将被创建。
参数：...
Additional arguments. Most methods pass them on to the ReadCounts method.
额外的参数。大多数方法通过ReadCounts方法。
Details
详情----------Details----------
The length of binding and support regions can either be given as a single value or as a range of possible values (by providing the minimum and maximum). In the latter case the cross-correlation between read counts on forward and reverse strand will be used to determine a value within that range. Note that this may lead sub-optimal choices of binding and support region length.
约束力和支持区域的长度，既可以作为一个单一的值或可能值的范围（通过提供的最低和最高）。在后一种情况下，正向和反向链上的只读计数之间的交叉相关，将被用来确定在这个范围内的值。请注意，这可能会导致次优选择的约束力和支持区域的长度。
值----------Value----------
An object of class BindScore if compress = FALSE, otherwise an object of class RLEBindScore
一个类的对象BindScore如果compress = FALSE，否则一个类的对象RLEBindScore
方法----------Methods----------
data = "ANY" Default method to handle all forms of input not explicitly handled by their own method. In particular this will be used for objects of class AlignedRead and data.frame but it will handle class for which a strandPileup method is available.
数据=“任何”默认的方法来处理所有形式没有明确自己的方法处理输入。特别是，这将用于类对象AlignedRead和data.frame但它会处理类strandPileup方法可用。
data = "character" Allows to use a file name referring to a file of mapped sequence reads as input.
数据=“字符”允许使用一个文件名指的是一个文件映射序列作为输入读取。
data = "matrix" Uses a matrix of read counts (for a single chromosome) as input.
作为输入数据=“矩阵”使用的阅读计数矩阵（一条染色体）。
data = "ReadCounts" This methods implements the peak calling algorithm. Other methods will typically reformat their input and pass it on to this method.
数据=“ReadCounts”这种方法实现峰值调用算法。其他方法通常会格式化他们的意见，并把它传递给这个方法。
参见----------See Also----------
simpleNucCall for an interface with nucleosome specific defaults. This function uses strandPileup, startScore, getCutoff and pickPeak. See the help pages of these functions for additional detail on the individual steps involved. See getBindLen
simpleNucCall与核小体的具体默认的接口。此功能使用strandPileup，startScore，getCutoff和pickPeak。看到这些功能的帮助页面上所涉及的各个步骤的更多细节。看到getBindLen
举例----------Examples----------
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 <- callBindingSites(readPile, bind=147, support=20, background=2000, plot=FALSE)
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 14:51:16
