makeoutput(hopach)
makeoutput()所属R语言包：hopach
function to write a text file with hopach output
函数写hopach输出一个文本文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The function makeoutput takes a data matrix and corresponding hopach clustering output, plus possibly bootstrap resampling output, and makes a table summarizing the clustering results. The table is written to a tab delimited text file.
功能makeoutput数据矩阵和相应的hopach聚类输出，加上可能引导重采样输出，使总结的聚类结果表。表被写入到一个制表符分隔的文本文件。
用法----------Usage----------
makeoutput(data, hopachobj, bootobj = NULL, file = "HOPACH.out",
gene.names = NULL)
参数----------Arguments----------
参数：data
data matrix, data frame or exprSet of gene expression measurements. Typically, each column corresponds to an array, and each row corresponds to a gene. For clustering arrays, the arrays appear in the rows and the genes in the columns. All values must be numeric. Missing values are ignored.
数据矩阵，基因表达测量的数据框或exprSet。通常情况下，每一列对应一个数组，每一行对应一个基因。为聚类阵列，阵列中的行和列中的基因出现。所有的值必须是数字。遗漏值将被忽略。
参数：hopachobj
output of the hopach function.
hopach函数的输出。
参数：bootobj
optional output of boothopach or bootmedoids - a matrix of bootstrap estimated cluster membership probabilities, with a row for each row in data and a column for each cluster.
可选的输出boothopach或bootmedoids - data和每个聚类列的每一行与行，估计引导聚类成员概率矩阵。
参数：file
filename for the table produced.
表的文件名产生。
参数：gene.names
optional names or annotations for the genes (arrays), which can be different from the row names of data
可选名称或注释的基因（阵列），它可以是从data行名称不同
Details
详情----------Details----------
The output table contains information about the rows of data: Index, UID and Name; the main cluster results: Cluster Number, Cluster Label (from hopach), and Cluster Level Order (the ordering of the elements in the level of the hopach tree at which the main clusters were identified); and the final level of the tree: Final Label, and Final Order (the ordering of elements in the final level of the tree). Sorting this table on Index results in the rows having the same order as in data. Sorting on Cluster Level Order results in the rows being ordered by cluster, and then within cluster based on the value of the argument ord to hopach (default is distance to the medoid). Sorting on Final Level Order results in the rows being ordered as in the leaves of the hopach tree, where clusters are still ordered and elements near each other in the ordering will have small pairwise distances.
输出表中包含行的信息data：指数，UID和名称;主要的聚类结果：聚类，聚类标签（从hopach），和聚类级别的顺序（元素的顺序hopach树被确定的主要聚类）的水平;和树的最后一级：最后一个标签，并最终令“（元素在树的最后一级的顺序）。此表上具有相同的顺序在数据中的行的索引结果的排序。聚类级别的顺序结果的排序由聚类命令行，然后在聚类内的参数值的基础上ordhopach（默认是距离的medoid）。 hopach树，聚类仍然排列在订购将有小成对距离和元素彼此靠得很近的叶子被下令行的最后一级订购结果排序。
值----------Value----------
The function makeoutput has no value. It writes a tab delimited text file to the current working directory.
功能makeoutput有没有价值。制表符分隔的文本文件写入到当前工作目录。
注意----------Note----------
Thank you to Karen Vranizan <vranizan@uclink.berkeley.edu> for helping to write this function.
感谢您对的卡伦Vranizan <vranizan@uclink.berkeley.edu>帮助编写这个函数。
作者（S）----------Author(s)----------
Katherine S. Pollard <kpollard@gladstone.ucsf.edu>
参考文献----------References----------
参见----------See Also----------
hopach, boothopach, bootmedoids
hopach，boothopach，bootmedoids
举例----------Examples----------
#25 variables from two groups with 3 observations per variable[25两组每3个变量观测变量]
mydata<-rbind(cbind(rnorm(10,0,0.5),rnorm(10,0,0.5),rnorm(10,0,0.5)),cbind(rnorm(15,5,0.5),rnorm(15,5,0.5),rnorm(15,5,0.5)))
dimnames(mydata)<-list(paste("Var",1:25,sep=""),paste("Exp",1:3,sep=""))
mydist<-distancematrix(mydata,d="cosangle") #compute the distance matrix.[计算距离矩阵。]
#clusters and final tree[聚类和最终树]
clustresult<-hopach(mydata,dmat=mydist)
#bootstrap resampling[举重采样]
myobj<-boothopach(mydata,clustresult)
#write output file[将输出写入文件]
makeoutput(mydata,clustresult,myobj)
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。
|
发表于 2012-2-25 21:47:01
