emfit(EBarrays)
emfit()所属R语言包：EBarrays
Implements EM algorithm for gene expression mixture model
实现的EM算法对基因表达的混合模型
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Implements the EM algorithm for gene expression mixture model
实现对基因表达的混合模型的EM算法
用法----------Usage----------
emfit(data,
family,
hypotheses,
...)
用法----------Usage----------
emfit(data,
family,
hypotheses,
cluster,
type=2,
criterion="BIC",
cluster.init = NULL,
num.iter = 20,
verbose = getOption("verbose"),
optim.control = list(),...)
参数----------Arguments----------
参数：data
a matrix
矩阵
参数：family
an object of class “ebarraysFamily” or a character string which can be coerced to one. Currently, only the characters "GG" and "LNN", and "LNNMV" are valid. For LNNMV, a groupid is required. See below. Other families can be supplied by constructing them explicitly.
类的“ebarraysFamily”或可以强制一个字符串对象。目前，只有字符“的GG”和“LNN型”，“LNNMV”是有效的。为LNNMV，groupid需要。见下文。其他家庭可以提供他们明确由建设。
参数：hypotheses
an object of class “ebarraysPatterns” representing the hypotheses of interest. Such patterns can be generated by the function ebPatterns
类“ebarraysPatterns”代表利益的假设对象。这种模式可以产生的功能ebPatterns
参数：cluster
if type=1, cluster is a vector specifying the fixed cluster membership for each gene; if type=2, cluster specifies the number of clusters to be fitted
如果type= 1，cluster是指定固定的聚类成员每个基因的向量;如果type= 2，cluster指定聚类安装
参数：type
if type=1, the cluster membership is fixed as input cluster; if type=2, fit the data with a fixed number of clusters
如果type= 1，聚类成员是固定的作为输入cluster;type= 2，适合固定数量的聚类数据
参数：criterion
only used when type=2 and cluster contains more than one integers. All numbers of clusters provided in cluster will be fitted and the one that minimizes criterion will be returned. Possible values now are "BIC", "AIC" and "HQ"
仅当type= 2cluster包含多个整数。 cluster提供的所有数字聚类将配备，最大限度地减少的criterion将被退回。现在可能值“的BIC”，“工商局”和“总部”
参数：cluster.init
only used when type=2. Specify the initial clustering membership.
只用了type= 2时。指定初始的聚类成员。
参数：num.iter
number of EM iterations
数量的EM迭代
参数：verbose
logical or numeric (0,1,2) indicating desired level of information printed for the user
逻辑或数字（0,1,2）为用户打印的信息显示所需的水平
参数：optim.control
list passed unchanged to optim for finer control
名单通过不变optim更好的控制
参数：...
groupid: an integer vector indicating which group each sample belongs to, required in the “LNNMV” model. It does not depend on “hypotheses”.
groupid：一个整数向量表示每个样品属于哪一组，需要在“LNNMV”模式。它不依赖于“假设”。
值----------Value----------
an object of class “ebarraysEMfit”, that can be summarized by show() and used to generate posterior probabilities using postprob
类“ebarraysEMfit”，可以概括show()用来生成后验概率的对象使用postprob
作者（S）----------Author(s)----------
Ming Yuan, Ping Wang, Deepayan Sarkar, Michael Newton, and
Christina Kendziorski
参考文献----------References----------
On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. Journal of Computational Biology 8:37-52.
On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statistics in Medicine 22:3899-3914.
Parametric Empirical Bayes Methods for Microarrays in The analysis of gene expression data: methods and software. Eds. G. Parmigiani, E.S. Garrett, R. Irizarry and S.L. Zeger, New York: Springer Verlag, 2003.
Detecting differential gene expression with a semiparametric hierarchical mixture model. Biostatistics 5: 155-176.
gene clustering and differential expression identification. Biometrics 62(4): 1089-1098.
参见----------See Also----------
ebPatterns, ebarraysFamily-class
ebPatterns，ebarraysFamily-class
举例----------Examples----------
data(sample.ExpressionSet) ## from Biobase[＃从BIOBASE]
eset <- exprs(sample.ExpressionSet)
patterns <- ebPatterns(c("1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1",
"1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2"))
gg.fit <- emfit(data = eset, family = "GG", hypotheses = patterns, verbose = TRUE)
show(gg.fit)
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 16:52:08
