SnpSet-methods(oligoClasses)
SnpSet-methods()所属R语言包：oligoClasses
Accessors and methods for SnpSet objects
accessor和SnpSet对象方法
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Utility functions for accessing data in SnpSet objects.
SnpSet对象访问数据的实用功能。
用法----------Usage----------
calls(object)
calls(object) <- value
confs(object, transform=TRUE)
confs(object) <- value
参数----------Arguments----------
参数：object
A SnpSet object.
一个SnpSet对象。
参数：transform
Logical. Whether to transform the integer representation of the confidence score (for memory efficiency) to a probability. See details.
逻辑。是否改造的信心分数的整数表示（记忆效率）的概率。查看详情。
参数：value
A matrix.
矩阵。
Details
详情----------Details----------
calls returns the genotype calls. CRLMM stores genotype calls as integers (1 - AA; 2 - AB; 3 - BB).
calls返回的基因型调用。 CRLMM商店基因型称为整数（1 - AA; 2 - AB公司; 3 - BB的）。
confs returns the confidences associated with the genotype calls. The current implementation of CRLMM stores the confidences as integers to save memory on disk by using the transformation:
confs返回与基因型调用关联的机密。目前实施的CRLMM存储整数保存在磁盘上的内存使用改造的信心：
round(-1000*log2(1-p)),
轮（-1000 *为log2（1-P）），
where 'p' is the posterior probability of the call. confs is a convenience function that transforms the integer representation back to a probability. Note that if the assayData elements of the SnpSet objects are ff_matrix or ffdf, the confs function will return a warning. For such objects, one should first subset the ff object and coerce to a matrix, then apply the above conversion. The function snpCallProbability for the callProbability slot of SnpSet objects. See the examples below.
其中“P”是呼叫后验概率。 confs是一个方便的功能转换的整数表示回到一个概率。注意如果SnpSet对象assayData元素，ff_matrix或ffdf，confs函数将返回一个警告。对于这样的对象，应该第一子集ff对象，并要挟矩阵，然后应用上述转换。函数snpCallProbabilitycallProbabilitySnpSet对象插槽。见下面的例子。
checkOrder checks whether the object is ordered by chromosome and physical position, evaluating to TRUE or FALSE.
checkOrder检查对象是否是由染色体和物理位置排列，评估为TRUE或FALSE。
注意----------Note----------
Note that the replacement method for confs<- expects a matrix of probabilities and will automatically convert the probabilities to an integer representation. See details for the conversion.
请注意confs<-置换法预计的概率矩阵，并会自动转换到一个整数表示的概率。详情请参阅转换。
The accessor snpCallProbability is an accessor for the 'callProbability' element of the assayData. The name can be misleading, however, as the accessor will not return a probability if the call probabilities are represented as integers.
存取snpCallProbability是存取callProbability元素assayData。可能会产生误导的名称，但是，作为存取不会返回，如果调用的概率表示为整数的概率。
参见----------See Also----------
See addFeatureAnnotation for adding chromosome, physical position, and an indicator for whether the marker is polymorphic to the featureData slot of a SnpSet object.
看到addFeatureAnnotation加入染色体，物理位置，是否标记多态性featureDataSnpSet对象插槽指标。
The helper functions p2i converts probabilities to integers and i2p converts integers to probabilities.
辅助函数p2i概率转换成整数和i2p转换整数概率。
See order and checkOrder.
看到order和checkOrder。
举例----------Examples----------
theCalls <- matrix(sample(1:3, 20, rep=TRUE), nc=2)
p <- matrix(runif(20), nc=2)
integerRepresentation <- matrix(as.integer(round(-1000*log(1-p))), 10, 2)
obj <- new("SnpSet", call=theCalls, callProbability=integerRepresentation)
calls(obj)
p2 <- confs(obj)
dimnames(p2) <- NULL
all.equal(p2, p) ## small differences due to rounding[＃小的差异，由于四舍五入]
int <- snpCallProbability(obj) ## not necessarily a probability[＃不一定概率]
p3 <- i2p(int) ## to convert back to a probability[＃转换回一个概率]
all.equal(p3, p2)
int <- snpCallProbability(obj) ## not necessarily a probability[＃不一定概率]
p3 <- i2p(int) ## to convert back to a probability[＃转换回一个概率]
all.equal(p3, p2)
## example using ff[＃例如使用FF]
if(require(ff)){
ldPath(tempdir())
integerRepresentation <- initializeBigMatrix("tmp", 10, 2)
for(j in 1:2) integerRepresentation[, j] <- as.integer(round(-1000*log(1-p[, j])))
integerRepresentation
obj <- new("SnpSet", call=theCalls, callProbability=integerRepresentation)
calls(obj)
res <- tryCatch(confs(obj), error=function(e) NULL)
is.null(res)
integerRepresentation <- snpCallProbability(obj)
##coerce to matrix by subsetting desired rows and columns (here we choose all rows and columns)[＃强迫矩阵子集所需的行和列（在这里我们选择的所有行和列）]
integerRepresentation <- integerRepresentation[,]
p3 <- oligoClasses:::i2p(integerRepresentation)
dimnames(p3) <- NULL
all.equal(p2, p3)
}
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 08:11:52
