aCGH(aCGH)
aCGH()所属R语言包：aCGH
Class aCGH
类aCGH
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Objects of this class represent batch of arrays of Comparative Genomic Hybridization data. In addition to that, there are slots for representing phenotype and various genomic events associated with aCGH experiments, such as transitions, amplifications, aberrations, and whole chromosomal gains and losses. Currently objects of class aCGH are represented as S3 classes which are named list of lists with functions for accessing elements of that list. In the future, it's anticipated that aCGH objects will be implemented using S4 classes and methods.
这个类的对象代表的一批阵列比较基因组杂交数据。此外，有代表型和aCGH实验，如过渡，扩增，畸变，和整个染色体的收益和损失，相关的各种基因事件的插槽。目前aCGH类的对象代表作为S3的班被命名为访问该列表中的元素与功能列表。在未来，它预计将实施aCGH对象，使用S4类和方法。
Details
详情----------Details----------
One way of creating objects of class aCGH is to provide the two mandatory arguments to create.aCGH function: log2.ratios and clones.info. Alternatively aCGH object can be created using aCGH.read.Sprocs that reads Sproc data files and creates object of type aCGH.
一类aCGH创建对象的方式是提供两个强制性参数create.aCGH功能：log2.ratios和clones.info。另外aCGH对象可以使用aCGH.read.Sprocs读取存储过程的数据文件，并创建aCGH类型的对象。
值----------Value----------
参数：log2.ratios
Data frame containing the log2 ratios of copy number changes; rows correspond to the clones and the columns to the samples (Mandatory).
数据框包含log2拷贝数变化的比率;行对应的克隆和列的样本（强制性）。
参数：clones.info
Data frame containing information about the clones used for comparative genomic hybridization. The number of rows of clones.info has to match the number of rows in log2.ratios (Mandatory).
数据框包含的信息用于比较基因组杂交克隆。 clones.info匹配log2.ratios（强制性）中的行数，行数。
参数：phenotype
Data frame containing phenotypic information about samples used in the experiment generating the data. The number of rows of phenotype has to match the number of columns in log2.ratios (Optional).
数据框包含有关生成数据的实验中使用的样品的表型信息。 phenotypelog2.ratios（可选）中的列数相匹配的行数。
参数：log2.ratios.imputed
Data frame containing the imputed log2 ratios. Calculate this using impute.lowess function; look at the examples below (Optional).
数据框包含估算的log2比率。使用impute.lowess函数计算;看看下面的例子（可选）。
参数：hmm
The structure of the hmm element is described in hmm. Calculate this using find.hmm.states function; look at the examples below (Optional).
描述hmm的HMM元素的结构。使用find.hmm.states函数计算;看看下面的例子（可选）。
参数：hmm
Similar to the structure of the hmm element. Calculate this using mergeHmmStates function; look at the examples below (Optional).
类似HMM元素的结构。使用mergeHmmStates函数计算;看看下面的例子（可选）。
参数：sd.samples
The structure of the sd.samples element is described in computeSD.Samples. Calculate this using computeSD.Samples function; look at the examples below (Optional). It is prerequisite that the hmm states are estimated first.
的sd.samples元素的结构描述computeSD.Samples。使用computeSD.Samples函数计算;看看下面的例子（可选）。这是前提的HMM状态估计第一。
参数：genomic.events
The structure of the genomic.events element is described in find.genomic.events. Calculate this using find.genomic.events function; look also at the examples below. It is prerequisite that the hmm states and sd.samples are computed first. The genomic.events is used widely in variety of plotting functions such as plotHmmStates, plotFreqStat, and plotSummaryProfile.
的genomic.events元素的结构描述find.genomic.events。计算使用find.genomic.events功能，看看下面的例子也。先决条件是，首先计算HMM的状态和sd.samples。 genomic.events被广泛用于各种绘图功能，如plotHmmStates，plotFreqStat，plotSummaryProfile。
参数：dim.aCGH
returns the dimensions of the aCGH object: number of clones by number of samples.
返回的aCGH对象的尺寸：样本数量的克隆数。
参数：num.clones
number of clones/number of rows of the log2.ratios data.frame.
克隆数/的log2.ratios数据框的行数。
参数：nrow.aCGH
same as num.clones.
相同num.clones。
参数：is.aCGH
tests if its argument is an object of class aCGH.
测试，如果它的参数是一个类aCGH的对象。
参数：num.samples
number of samples/number of columns of the log2.ratios data.frame.
样本数/的log2.ratios数据框的列数。
参数：nrow.aCGH
same as num.samples.
相同num.samples。
参数：num.chromosomes
number of chromosomes processed and stored in the aCGH object.
处理的染色体数目和在aCGH对象存储。
参数：clone.names
returns the names of the clones stored in the clones.info slot of the aCGH object.
返回在的aCGH对象clones.info插槽存储克隆的名称。
参数：row.names.aCGH
same as clone.names.
相同clone.names。
参数：sample.names
returns the names of the samples used to create the aCGH object. If the object is created using aCGH.read.Sprocs, these are the file names of the individual arrays.
返回aCGH对象用来创建样品的名称。如果使用aCGH.read.Sprocs，这些都是单个阵列中的文件名创建对象。
参数：col.names.aCGH
same as sample.names.
相同sample.names。
参数：[.aCGH
subsetting function. Works the same way as [.data.frame.
子集的功能。工程[.data.frame同样的方式。
Most of the functions/slots listed above have assignment operators '<-' associated with them.
最上面列出的功能/插槽有赋值运算符“< - ”与他们有联系。
注意----------Note----------
clones.info slot has to contain a list with at least 4 columns: Clone (clone name), Target (unique ID, e.g. Well ID), Chrom (chromosome number, X chromosome = 23 in human and 20 in mouse, Y chromosome = 24 in human and 21 in mouse) and kb (kb position on the chromosome).
clones.info插槽有至少包含4列列表：克隆（克隆的名字），目标（唯一的ID，如井编号），CHROM（染色体数目，X染色体在人类和= 23，y鼠标20染色体= 24在人类和小鼠21）和KB（KB在染色体上的位置）。
作者（S）----------Author(s)----------
Peter Dimitrov
参见----------See Also----------
aCGH.read.Sprocs, find.hmm.states, computeSD.Samples, find.genomic.events, plotGenome, plotHmmStates, plotFreqStat, plotSummaryProfile
aCGH.read.Sprocs，find.hmm.states，computeSD.Samples，find.genomic.events，plotGenome，plotHmmStates，plotFreqStat，plotSummaryProfile
举例----------Examples----------
## Creating aCGH object from log2.ratios and clone info files[＃创建log2.ratios和克隆文件aCGH对象]
## For alternative way look at aCGH.read.Sprocs help[＃替代aCGH.read.Sprocs帮助的方式看看]
datadir <- system.file(package = "aCGH")
datadir <- paste(datadir, "/examples", sep="")
clones.info <-
read.table(file = file.path(datadir, "clones.info.ex.txt"),
header = TRUE, sep = "\t", quote="", comment.char="")
log2.ratios <-
read.table(file = file.path(datadir, "log2.ratios.ex.txt"),
header = TRUE, sep = "\t", quote="", comment.char="")
pheno.type <-
read.table(file = file.path(datadir, "pheno.type.ex.txt"),
header = TRUE, sep = "\t", quote="", comment.char="")
ex.acgh <- create.aCGH(log2.ratios, clones.info, pheno.type)
## Printing, summary and basic plotting for objects of class aCGH[印刷，总结和基本绘图类aCGH对象]
data(colorectal)
colorectal
summary(colorectal)
sample.names(colorectal)
phenotype(colorectal)
plot(colorectal)
## Subsetting aCGH object[＃子集aCGH对象]
colorectal[1:1000, 1:30]
## Imputing the log2 ratios [＃归咎于的log2比率]
log2.ratios.imputed(ex.acgh) <- impute.lowess(ex.acgh)
## Determining hmm states of the clones[克隆＃确定HMM状态]
## WARNING: Calculating the states takes some time[＃警告：计算状态，需要一些时间]
##in the interests of time, hmm-finding function is commented out[＃在时间的利益，HMM发现功能被注释掉]
##instead the states previosuly save are assigned[＃，而不是美国previosuly保存分配]
##hmm(ex.acgh) <- find.hmm.states(ex.acgh)[＃HMM（ex.acgh）< - find.hmm.states（ex.acgh的）]
hmm(ex.acgh) <- ex.acgh.hmm
hmm.merged(ex.acgh) <-
mergeHmmStates(ex.acgh, model.use = 1, minDiff = .25)
## Calculating the standard deviations for each array[＃计算每个阵列的标准偏差]
sd.samples(ex.acgh) <- computeSD.Samples(ex.acgh)
## Finding the genomic events associated with each sample[＃查找每个样品的基因组事件]
genomic.events(ex.acgh) <- find.genomic.events(ex.acgh)
## Plotting and printing the hmm states[＃绘图和打印HMM状态]
plotHmmStates(ex.acgh, 1)
pdf("hmm.states.temp.pdf")
plotHmmStates(ex.acgh, 1)
dev.off()
## Plotting summary of the sample profiles[＃绘制简易的样本概况]
plotSummaryProfile(colorectal)
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 10:58:35
