cateGOry(Category)
cateGOry()所属R语言包：Category
Construct a category membership matrix from a list of gene
构建从基因列表中的一类隶属度矩阵
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The function constructs a category membership matrix, such as used by applyByCategory, from a list of gene identifiers and their annotated GO categories. For each of the GO categories stated in categ, all less specific terms (ancestors) are also included, thus one need only obtain the most specific set of GO term mappings, which can be obtained from Bioconductor annotation packages or via biomaRt. The ancestor relationships are obtained from the GO.db package.
函数构造一个类的隶属度矩阵，如使用applyByCategory，从基因标识和其注释的GO类别的列表。对于每个表示在categ GO类别，都不太具体条款（祖先）也包括在内，因此，人们只需要取得好术语的映射，它可以从Bioconductor注解包或通过获得的最具体的设置 biomaRt。祖先的关系得到了GO.db包。
用法----------Usage----------
cateGOry(x, categ, sparse=FALSE)
参数----------Arguments----------
参数：x
Character vector with (arbitrary) gene identifiers. They will be used for the column names of the resulting matrix.
（任意）基因标识的特征向量。它们将被用于矩阵的列名。
参数：categ
A character vector of the same length as x with GO annotations for the genes in x. If a gene has multiple GO annotations, it is expected to occur multiple times in x, once for each different annotation.
特征向量的长度相同x去x基因注解。如果一个基因有多个好注释，它预计将出现在x多次，一次为每个不同的注解。
参数：sparse
Logical. Currently, this is ignored. This argument might be used in future versions of the function to result in returning a sparse matrix representation.
逻辑。目前，这个被忽略。这种说法可能用于未来版本的功能，导致返回一个稀疏矩阵表示。
Details
详情----------Details----------
Requires the GO package.
需要GO包。
For some subsequent analyses, it is useful to remove categories that have only a small number of members. Use the normal matrix subsetting syntax for this, see example.
对于一些后续的分析，它是有用的删除，只有少数成员的类别。使用正常的矩阵子集语法，看到的例子。
If a GO category in categ is not found in the GO annotation package, a warning will be generated, and no ancestors for that GO category are added (but that category itself will be part of the returned adjacency matrix).
如果在categ go目录没有发现GO注释包，将生成警告，并加入该GO类别没有祖先（但这一类本身将返回的邻接矩阵的一部分）。
值----------Value----------
The adjacency matrix of the bipartite category membership graph, rows are categories and columns genes.
双边类成员图的邻接矩阵，行类和列的基因。
作者（S）----------Author(s)----------
W. Huber
参见----------See Also----------
applyByCategory
applyByCategory
举例----------Examples----------
g = cateGOry(c("CG2671", "CG2671", "CG2950"),
c("GO:0000074", "GO:0001738", "GO:0003676"))
g
rownames(g)
colnames(g)
rowSums(g) ## number of genes in each category[＃在每个类别中的基因数目]
## Filter out categories with less than minMem members.[＃过滤掉小于minMem成员的类别。]
## This is toy data, in real applications, a number higher[＃这是玩具的数据，在实际应用中，数字高]
## than 2 will be more appropriate.[2＃比会更合适。]
minMemb = 2
g[rowSums(g)>=minMemb,,drop=FALSE ]
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 14:05:50
