cghRaw(CGHbase)
cghRaw()所属R语言包：CGHbase
Class to contain and describe raw or normalized array comparative genomic hybridization data.
类包含和描述原料或归阵列比较基因组杂交数据。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Container for aCGH data and experimental metadata. cghRaw class is derived from eSet, and requires a matrix named copynumber as assayData member. Furthermore, columns named Chromosome, Start, and End are required as featureData members, containing feature position information.
aCGH数据和实验的元数据的容器。 cghRaweSet类派生，并要求名为copynumber作为assayData成员的矩阵。此外，列名为Chromosome，Start，功能End需要featureData成员，包含位置信息。
延伸----------Extends----------
Directly extends class eSet.
直接延伸类eSet。
创建对象----------Creating Objects----------
new('cghRaw', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], featureData = [AnnotatedDataFrame], ...)
new('cghRaw', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], featureData = [AnnotatedDataFrame], ...)
make_cghRaw is a function to convert a dataframe or textfile to an object of class cghRaw. The input should be either a dataframe or a tabseparated textfile (textfiles must contain a header). The first three columns should contain the name, chromosome and position in bp for each array target respectively. The chromosome and position column must contain numbers only. Following these is a column with log2 ratios for each of your samples. If the input type is a textfile, missing values should be represented as 'NA' or an empty field.
make_cghRaw是一个功能类cghRaw对象，转换dataframe或文本文件。输入应该是一个dataframe或tabseparated文本文件（文本文件必须包含一个头）。前三列应包含的名称，染色体和BP分别为每个阵列目标的位置。染色体和位置列必须只包含数字。以下这些是log2每个样品的比列。如果输入类型是文本文件，遗漏值应表示为“无”或空场。
插槽----------Slots----------
Inherited from eSet:
继承自eSet
assayData: Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain a matrix copynumber with rows represening array probes and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may
assayData：包含与同等尺寸的矩阵，列数等于nrow(phenoData)。 assayData必须包含一个矩阵与represening阵探针和列代表样本行copynumber。相同大小的附加矩阵（例如，代表测量误差）
phenoData: See eSet
phenoData：见eSet
featureData: An AnnotatedDataFrame with columns Chromosome, Start, and End containing array element position
featureData：AnnotatedDataFrame同列Chromosome，Start，End包含数组元素的位置
experimentData: See eSet
experimentData：见eSet
annotation: See eSet
annotation：见eSet
方法----------Methods----------
Class-specific methods.
类的具体方法。
copynumber(cghRaw), copynumber(cghRaw,matrix)<- Access and set elements named copynumber in the AssayData-class
copynumber(cghRaw)，copynumber(cghRaw,matrix)<-访问集合中元素的名为copynumberAssayData-class
chromosomes, bpstart, bpend Access the chromosomal positions stored in featureData
chromosomes，bpstart，bpend访问featureData存储的染色体位置
plot.cghRaw Create a plot containing log2ratios ordered by chromosomal position
plot.cghRaw含有染色体的位置排列log2ratios创建一个图
See eSet for derived methods. Annotation functionality is not yet supported.
看到eSet派生的方法。注解功能目前还不支持。
作者（S）----------Author(s)----------
Sjoerd Vosse
参见----------See Also----------
eSet-class, cghSeg-class, cghCall-class
eSet-class，cghSeg-class，cghCall-class
举例----------Examples----------
# create an instance of cghRaw[创建的cghRaw实例]
new("cghRaw")
# create an instance of cghRaw from a dataframe[创建从dataframe的一个实例cghRaw]
data(WiltingData)
cghobj <- cghRaw(WiltingData)
# plot the first sample[绘制第一个样本]
plot(cghobj[,1])
# first three chromosomes[第3染色体]
plot(cghobj[chromosomes(cghobj)==1,1])
# get the copynumber values of the third and fourth sample[获得的第三个和第四个样本copynumber值]
log2ratios <- copynumber(cghobj[,3:4])
# get the names of the samples[样品名称]
sampleNames(cghobj)
# get the names of the array elements[数组元素的名称]
featureNames(cghobj)
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 14:30:05
