CNSet-class(oligoClasses)
CNSet-class()所属R语言包：oligoClasses
Class "CNSet"
类“CNSet”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
CNSet is a container for intermediate data and parameters pertaining to allele-specific copy number estimation. Methods for CNSet objects, including accessors for linear model parameters and allele-specific copy number are included here.
CNSet是一个中间数据和有关的特定基因的拷贝数估计的参数的容器。这里包括的CNSet对象，包括线性模型参数和特定基因的拷贝数的存取方法。
类的对象----------Objects from the Class----------
An object from the class is not generally intended to be initialized by the user, but returned by the genotype function in the crlmm package.
从类对象不是一般的目的是由用户初始化但genotypecrlmm包的功能返回。
The following creates a very basic CNSet with assayData containing the required elements.
下面创建一个非常基本的CNSet用assayData包含必需的元素。
new(CNSet, alleleA=new("matrix"), alleleB=new("matrix"), call=new("matrix"), callProbability=new("matrix"), batch=new("factor"))
new(CNSet, alleleA=new("matrix"), alleleB=new("matrix"), call=new("matrix"), callProbability=new("matrix"), batch=new("factor"))
插槽----------Slots----------
batch: Object of class "factor" ~~
batch：Object类的"factor"~~
batchStatistics: Object of class "AssayData" ~~
batchStatistics：Object类的"AssayData"~~
assayData: Object of class "AssayData" ~~
assayData：Object类的"AssayData"~~
phenoData: Object of class "AnnotatedDataFrame" ~~
phenoData：Object类的"AnnotatedDataFrame"~~
featureData: Object of class "AnnotatedDataFrame" ~~
featureData：Object类的"AnnotatedDataFrame"~~
experimentData: Object of class "MIAME" ~~
experimentData：Object类的"MIAME"~~
annotation: Object of class "character" ~~
annotation：Object类的"character"~~
protocolData: Object of class "AnnotatedDataFrame" ~~
protocolData：Object类的"AnnotatedDataFrame"~~
.__classVersion__: Object of class "Versions" ~~
.__classVersion__：Object类的"Versions"~~
延伸----------Extends----------
Class "SnpSet", directly. Class "eSet", by class "SnpSet", distance 2. Class "VersionedBiobase", by class "SnpSet", distance 3. Class "Versioned", by class "SnpSet", distance 4.
类"SnpSet"，直接。类"eSet"，由类“SnpSet”，距离为2。类"VersionedBiobase"，由类“SnpSet”，距离3。类"Versioned"，由类“SnpSet”，距离4。
方法----------Methods----------
[ signature(x = "CNSet"): ...
[signature(x = "CNSet")...
A signature(object = "CNSet"): ...
一个signature(object = "CNSet")：...
A<- signature(object = "CNSet"): ...
一个< - signature(object = "CNSet")...
allele signature(object = "CNSet"): ...
的等位基因signature(object = "CNSet")：...
B signature(object = "CNSet"): ...
Bsignature(object = "CNSet")...
B<- signature(object = "CNSet"): ...
与B < - signature(object = "CNSet")...
batch signature(object = "CNSet"): ...
一批signature(object = "CNSet")...
batchNames signature(object = "CNSet"): ...
batchNamessignature(object = "CNSet")...
batchNames<- signature(object = "CNSet"): ...
batchNames < - signature(object = "CNSet")...
close signature(con = "CNSet"): ...
关闭signature(con = "CNSet")：...
coerce signature(from="CNSetLM"): ...
要挟signature(from="CNSetLM")...
coerce signature(from="CNSet"): ...
要挟signature(from="CNSet")...
corr signature(object = "CNSet", allele = "character"): ...
更正signature(object = "CNSet", allele = "character")...
flags signature(object="CNSet"): SNP flags
标志signature(object="CNSet")：SNP的标志
initialize signature(.Object = "CNSet"): ...
初始化signature(.Object = "CNSet")...
nu signature(object = "CNSet", allele = "character"): ...
NUsignature(object = "CNSet", allele = "character")...
open signature(con = "CNSet"): ...
打开signature(con = "CNSet")：...
phi signature(object = "CNSet", allele =
披的<code>签名（对象=“CNSet”，等位基因
sigma2 signature(object = "CNSet", allele = "character"): ...
sigma2signature(object = "CNSet", allele = "character")...
tau2 signature(object = "CNSet", allele = "character"): ...
tau2signature(object = "CNSet", allele = "character")...
作者（S）----------Author(s)----------
R. Scharpf
举例----------Examples----------
if(require("genomewidesnp6Crlmm")){
require("genomewidesnp6Crlmm")
fns <- c("SNP_A-2131660", "SNP_A-1967418", "SNP_A-1969580", "SNP_A-4263484",
"SNP_A-1978185", "SNP_A-4264431", "SNP_A-1980898", "SNP_A-1983139",
"SNP_A-4265735", "SNP_A-1995832")
theCalls <- matrix(2, nc=2, nrow=10)
A <- matrix(sample(1:1000, 20), 10,2)
B <- matrix(sample(1:1000, 20), 10,2)
p <- matrix(runif(20), nc=2)
theConfs <- round(-1000*log2(1-p))
## Batch can be defined by the scan date of the array[＃批处理可以定义数组扫描日期]
##or the 96 well chemistry plate from which the[＃或96以及化学板]
##samples were derived. Here we indicate that the two[＃样品而得。在这里，我们表明，两]
##samples were from the same batch.[＃样品从同一批次。]
batch <- rep(factor(1), ncol(A))
## each parameter is a R x C matrix, where the number[＃每个参数是一个R X C矩阵，这里的数字]
## of rows (R) corresponds to the number of features[＃行（R）对应的功能]
## and the number of columns (C) corresponds to the[＃和列数（C）对应于]
## number of batches. In this toy example, the[＃批次数。在这个玩具的例子，在]
## samples were assumed to be from the same batch.[＃样品被认为是从同一批次。]
## Ordinarily, one would have 50+ samples in a given[＃通常，人们会在给定的50 +样本]
## batch.[＃批处理。]
dns <- list(fns, batch="1")
obj <- new("CNSet",
alleleA=A,
alleleB=B,
call=theCalls,
callProbability=theConfs,
batch=as.character(rep(1, ncol(A))),
annotation="genomewidesnp6")
assayDataElementNames(batchStatistics(obj))
featureNames(obj) <- fns
## Accessors[＃存取]
calls(obj)
confs(obj)
A(obj)
B(obj)
featureData(obj) <- addFeatureAnnotation(obj)
isSnp(obj)
chromosome(obj)
position(obj)
}
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。
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发表于 2012-2-26 08:05:07
