IdClusters(DECIPHER)
IdClusters()所属R语言包：DECIPHER
Cluster Sequences By Distance
通过远程聚类序列
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Groups the sequences represented by a distance matrix into clusters of similarity.
到相似的聚类距离矩阵表示的序列。
用法----------Usage----------
IdClusters(myDistMatrix,
method = "UPGMA",
cutoff = -Inf,
showPlot = FALSE,
asDendrogram = FALSE,
myDNAStringSet = NULL,
add2tbl = FALSE,
dbFile = NULL,
verbose = TRUE)
参数----------Arguments----------
参数：myDistMatrix
A symmetric N x N distance matrix with the values of dissimilarity between N sequences.
对称NXNN序列之间的相异值的距离矩阵。
参数：method
An agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "complete", "single", "UPGMA", "average", "NJ" or "ML".
一个集聚的方法来使用。这应该是（一个明确的缩写）"complete"，"single"，"UPGMA"，"average"，"NJ"或"ML"。
参数：cutoff
A vector with the maximum branch length separating the sequences in the same cluster. If asDendrogram=TRUE then only one cutoff may be specified.
分行在同一个聚类中分离序列的最大长度的向量。如果asDendrogram=TRUE然后只有一个截止可以指定。
参数：showPlot
Logical specifying whether or not to plot the resulting dendrogram.
逻辑指定是否绘制生成的树状。
参数：asDendrogram
Logical. If TRUE the object returned is of class dendrogram.
逻辑。如果TRUE类dendrogram返回的对象是。
参数：myDNAStringSet
DNAStringSet used in the creation of myDistMatrix. Only necessary if method="ML".
DNAStringSet使用myDistMatrix创造。只有必要的，如果method="ML"。
参数：add2tbl
Logical or a character string specifying the table name in which to add the result.
逻辑或一个字符串，指定要在其中添加结果表名。
参数：dbFile
A connection to a SQLite database or character string giving the path to the database file. Only necessary if add2tbl is not FALSE.
一个SQLite数据库或数据库文件的路径的字符串的连接。只需要add2tbl如果不FALSE。
参数：verbose
Logical indicating whether to display progress.
逻辑表明是否显示进度。
Details
详情----------Details----------
Groups the input sequences into clusters using a set dissimilarities representing the distance between N sequences. Initially a phylogenetic tree is formed using the specified method. Then each leaf (sequence) of the tree is assigned to a cluster based on its branch lengths to the other leaves (sequences).
将使用代表N序列之间的距离的一组相异的聚类组的输入序列。最初形成使用指定的method进化树。然后在树的每个叶（序列）被分配到其他的叶子（序列）根据其分支长度聚类。
A number of different clustering methods are provided. The method (complete assigns clusters using complete-linkage so that sequences in the same cluster are no more than cutoff percent apart. The method single assigns clusters using single-linkage so that sequences in the same cluster are within cutoff of at least one other sequence in the same cluster. UPGMA or average (the default) assigns clusters using average-linkage which is a compromise between the sensitivity of complete-linkage clustering to outliers and the tendency of single-linkage clustering to connect distant relatives that do not appear to be closely related.
提供了许多不同的聚类方法。 （complete分配使用完整的联动，使在同一聚类的序列是不超过cutoff％外聚类的方法single使用单联动，使该序列在分配聚类的方法同一聚类内cutoff其他序列中至少有一个相同的聚类。UPGMA或average（默认值）指定聚类使用平均联动，这是一个妥协之间的灵敏度完整联动聚类异常和单联动聚类的倾向，连接不会出现是密切相关的远房亲戚。
NJ uses the Neighbor-Joining method proposed by Saitou and Nei that does not assume lineages evolve at the same rate (the molecular clock hypothesis). The NJ method is typically the most phylogenetically accurate of the above distance based methods. ML creates a neighbor-joining tree and then prints the negative log likelihood of the tree. Presently ML does not adjust the neighbor joining tree to maximize its likelihood.
NJ使用邻接法斋藤和Nei提出的，不承担谱系演化以同样的速度（分子钟假说）。 NJ方法通常是系统发育的最准确的上述距离的方法。 ML创建一个邻接树，然后打印出树的负对数似然。目前ML不调整邻接树，以最大限度地发挥其可能性。
If a add2tbl=TRUE then the resulting data.frame is added/updated into column(s) of the default table "DNA" in dbFile. If add2tbl is a character string then the result is added to the specified table name in dbFile. The added/updated column names are printed if verbose=TRUE.
如果add2tbl=TRUE然后由此产生的数据框添加/更新成列的默认表中的“DNA”在dbFile（S）。如果add2tbl是一个字符串，那么结果被添加到指定的表名dbFile。如果verbose=TRUE添加/更新的列名印。
值----------Value----------
If asDendrogram=FALSE (the default), returns a data.frame with a column for each cutoff specified. The row.names of the data.frame correspond to the dimnames of myDistMatrix. Each one of N sequences is assigned to one of M clusters. If asDendrogram=TRUE, returns an object of class dendrogram that can be used for further manipulation and plotting. Leaves of the dendrogram are randomly colored by cluster number.
如果asDendrogram=FALSE（默认值），返回每个指定的截止列数据框。数据框row.names，对应到myDistMatrixdimnames。 N序列中的每一个被分配到M聚类之一。如果asDendrogram=TRUE，返回一个对象的类dendrogram，可用于进一步的处理和绘图。叶的树状随机颜色的簇号。
作者（S）----------Author(s)----------
Erik Wright <a href="mailto ECIPHER@cae.wisc.edu">DECIPHER@cae.wisc.edu</a>
参考文献----------References----------
参见----------See Also----------
DistanceMatrix, Add2DB
DistanceMatrix，Add2DB
举例----------Examples----------
# using the matrix from the original paper by Saitou and Nei[从原来的文件，由斋藤和Nei使用矩阵]
m <- matrix(0,8,8)
m[2:8,1] <- c(7, 8, 11, 13, 16, 13, 17)
m[3:8,2] <- c(5, 8, 10, 13, 10, 14)
m[4:8,3] <- c(5, 7, 10, 7, 11)
m[5:8,4] <- c(8, 11, 8, 12)
m[6:8,5] <- c(5, 6, 10)
m[7:8,6] <- c(9, 13)
m[8,7] <- c(8)
# returns an object of class "dendrogram"[返回一个对象类“树状”]
myClusters <- IdClusters(m, cutoff=10, method="NJ", showPlot=TRUE, asDendrogram=TRUE)
# example of specifying a cutoff[例如，指定一个截止]
# returns a data frame[返回一个数据框]
IdClusters(m, cutoff=c(2,6,10,20))
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 16:19:40
