InputFrame-class(ddCt)
InputFrame-class()所属R语言包：ddCt
Working with SDM files
使用SDM文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The class InputFrame provides core functionalities to read gene and sample information from SDM files and calculate them with a ddCt algorithm.
的的类InputFrame提供核心功能读取基因样本SDM文件的信息和与DDCT算法的计算。
The function InputFrame reads the data given in the colums 'Detector','Sample' and 'Ct' of the specified SDM output files and stores them as a data.frame. An additional column including the respective filename is added.
的功能InputFrame读取的colums“探测器”提供的数据，样品和CT指定SDM的输出文件和它们存储数据框。增加一个额外的列，其中包括相应的文件名。
插槽----------Slots----------
coreData: Object of class "data.frame": Holds all the required data extracted from the SDM file
coreData："data.frame"：拥有所有的SDM文件中提取所需的数据对象类
files: Object of class "character" contains the source SDM files
files："character"类对象包含源SDM文件
方法----------Methods----------
[,[[,\$ signature(x = "InputFrame"): primitive accessors. Returns an object of InputFrame-class with the subset data.
[，[，\ $signature(x = "InputFrame")：原始的存取。返回InputFrame-class与子集的数据对象。
names signature(x = "InputFrame"): returns the column names in this SDM object
SDM的对象在这名signature(x = "InputFrame")：返回的列名
ddCtExpression signature(object = "InputFrame"): runs a ddCt algorithm with this SDM object and returns a object of class ddCtExpression
ddCtExpressionsignature(object = "InputFrame")：运行这个SDM对象1 DDCT算法，并返回一个对象的类ddCtExpression
fileNames signature(object="InputFrame"): returns the source SDM file names.
文件名signature(object="InputFrame")：返回SDM的源文件名。
detectorNames signature(object = "InputFrame"): returns the detector names in this SDM object
detectorNamessignature(object = "InputFrame")：返回在此SDM对象的探测器名称
detectorNames<- signature(object = "InputFrame", value = "character"): replaces the detector names in this SDM object
detectorNames < - signature(object = "InputFrame", value = "character")：取代SDM的对象在这个探测器的名称
sampleNames signature(object = "InputFrame"): returns the sample names in this SDM object
sampleNamessignature(object = "InputFrame")：返回在此SDM对象样本名
sampleNames<- signature(object = "InputFrame", value = "character"): replaces the sample names in this SDM object
sampleNames < - signature(object = "InputFrame", value = "character")：替换在此SDM对象样本名
uniqueDetectorNames signature(object = "InputFrame"): returns a vector of unique detector names in this SDM object
uniqueDetectorNamessignature(object = "InputFrame")：返回在此SDM对象的一个独特的探测器名称的向量
uniqueDetectorNames<- signature(object = "InputFrame", target = "missing", value = "character"): replaces all detector names given by the 'names' attribute in 'value' with new detector names
uniqueDetectorNames < - signature(object = "InputFrame", target = "missing", value = "character")：价值，名称属性名称与新的探测器名称取代所有探测器
uniqueDetectorNames<- signature(object = "InputFrame", target = "character", value = "character"): replaces all detector names given by 'target' with new detector names
uniqueDetectorNames < - signature(object = "InputFrame", target = "character", value = "character")：“目标”的名称与新的探测器名称取代所有探测器
uniqueSampleNames<- signature(object = "InputFrame", target = "missing", value = "character"): replaces all sample names given by the 'names' attribute in 'value' with new sample names
uniqueSampleNames < - signature(object = "InputFrame", target = "missing", value = "character")“：在”价值“，”名称“属性与新样本名替换所有样品名
uniqueSampleNames<- signature(object = "InputFrame", target = "character", value = "character"): replaces all sample names given by 'target' with new sample names
uniqueSampleNames < - signature(object = "InputFrame", target = "character", value = "character")：取代所有样品的名称由“目标”与新样本名
uniqueSampleNames signature(object = "InputFrame"): returns a vector of unique sample names in this SDM object
uniqueSampleNamessignature(object = "InputFrame")：返回SDM的对象，在这个独特的样本名向量
removeSample signature(object = "InputFrame", sample="character"): removes the sample(s) specified from the InputFrame object
removeSamplesignature(object = "InputFrame", sample="character")：删除（S）从InputFrame对象指定的样品
replaceDetector signature(object = "InputFrame", target="character", value="character"): replace the detectors equal to the target with the value. Both target and value can be vectors of the same length, then the replace takes place iteratively.
replaceDetectorsignature(object = "InputFrame", target="character", value="character")：更换探测器等于目标与价值。既target和value可以是相同长度的向量，然后替换发生反复。
replaceSample signature(object = "InputFrame", target="character", value="character"): replace the samples equal to the target with the value. Both target and value can be vectors of the same length, then the replace takes place iteratively.
replaceSamplesignature(object = "InputFrame", target="character", value="character")：更换平等的目标与价值的样品。既target和value可以是相同长度的向量，然后替换发生反复。
show signature(object="InputFrame"): pretty print of the InputFrame instance.
显示signature(object="InputFrame")：的InputFrame实例的漂亮的打印。
rightCensoring signature(object="InputFrame", threshold="numeric"): Right censoring the Ct value, which targets the data points above a certain value (threshold). High Ct values (higher than 40 or 45 by the rule of thumb) are often not accurate and may indicate too weak expression. The function performs the right censoring on the data and set the value above the threshold as NA (by default) or a given value. See the example.
rightCensoringsignature(object="InputFrame", threshold="numeric")：右设限的Ct值，它的目标一定值以上的数据点（threshold）。高CT值（高于40或45法则）往往是不准确的，并可能表明太软弱的表现。函数执行对数据的权利审查，并设置以上NA（默认）或给定值的阈值。见的例子。
coreData signature(object="InputFrame"): returns the data frame read from SDM file.
coreDatasignature(object="InputFrame")：返回从SDM文件读取数据框。
coreData<- signature(object="InputFrame"): replace the data frame read from SDM file.
coreData < - signature(object="InputFrame")：更换从SDM文件读取数据框。
Ct signature(object="InputFrame"): returns the Ct value of the SDM file.
CTsignature(object="InputFrame")：返回的SDM文件的Ct值。
Ct signature(object="InputFrame", value="numeric"):
CTsignature(object="InputFrame", value="numeric")：
作者（S）----------Author(s)----------
Rudolf Biczok <a href="mailto:mailto:r.biczok@dkfz.de">mailto:r.biczok@dkfz.de</a>, Jitao David
Zhang <a href="mailto:mailto:jitao_david.zhang@roche.com">mailto:jitao_david.zhang@roche.com</a>
参见----------See Also----------
SDMFrame function reads in data from SDM files. Data from SDM files is used to construct ddCtExpression objects to analyze differetial expression.
SDMFrame功能SDM文件的数据读取。 SDM文件的数据被用来构建ddCtExpression对象，分析全微分表达。
举例----------Examples----------
## read a SDM file[＃读SDM文件]
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt",
package="ddCt"))
## you can also write [＃你也可以写]
## sampdat <- new("SDMFrame",system.file("extdata", "Experiment1.txt",[＃sampdat < - 新（的“SDMFrame”。系统（“extdata”，“Experiment1.txt”]
## package="ddCt"))[＃包=“DDCT”））]
## use the getter methods[＃使用的getter方法]
sampleNames(sampdat)
## or the overloaded primitive accessors[＃或超载的原始存取]
sampdat[1:3,"Sample"]
## see all unique samples[＃看到所有独特的样品。]
uniqueSampleNames(sampdat)
## replace all sample names 'Sample1' and 'Sample2' in sampdat[＃替换所有样品名称的SAMPLE1“和”的sample2在sampdat的。]
## with 'NewSample1' and 'NewSample2'[＃NewSample1和NewSample2]
uniqueSampleNames(sampdat,c("Sample1","Sample2")) <- c("NewSample1","NewSample2")
uniqueSampleNames(sampdat)
## or use this syntax to replace the gene names[＃或使用此语法来取代基因名称]
uniqueDetectorNames(sampdat) <- c(Gene1="NewGene1", Gene2="NewGene2")
uniqueDetectorNames(sampdat)
## remove sample or detector[＃取出样品或探测器]
removeSample(sampdat, "Sample1")
removeDetector(sampdat, "Gene1")
## replace sample or detector[＃替换样品或探测器]
replaceSample(sampdat, "Sample1", "Sample0")
replaceDetector(sampdat, "Gene1", "PLCG1")
## right censoring the data[＃右删失数据]
rightCensoring(sampdat, 35)
rightCensoring(sampdat, 35, 35)
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 2012-2-25 16:17:39
