cb_test(Category)
cb_test()所属R语言包：Category
Chromosome Band Tree-Based Hypothesis Testing
染色体带的基于树的假设检验
译者：生物统计家园网 机器人LoveR
描述----------Description----------
cb_test is a flexible tool for discovering interesting chromosome bands relative to a selected gene list. The function supports local and global tests which can be carried out in a top down or bottom up fashion on the tree of chromosome bands.
cb_test是一个灵活的工具，发现有趣的染色体带相对选定的基因列表。功能支持本地和全球的测试，可以进行染色体带的树在一个自上而下或底部时尚起来。
用法----------Usage----------
cb_test(selids, chrtree, level, dir = c("up", "down"),
type = c("local", "global"), next.pval = 0.05,
cond.pval = 0.05, conditional = FALSE)
参数----------Arguments----------
参数：selids
A vector of gene IDs. The IDs should match those used to annotatate the ChrBandTree given by chrtree. In most cases, these will be Entrez Gene IDs.
一个基因标识的向量。标识应符合那些，用于annotatateChrBandTree给chrtree。在大多数情况下，这些将是Entrez基因标识。
参数：chrtree
A ChrBandTree object representing the chromosome bands and the mapping to gene identifiers. The genes in the ChrBandTree are limited to the universe of gene IDs specified at object creation time.
一个ChrBandTree对象代表的染色体带和基因标识的映射。在基因的ChrBandTree是有限的宇宙在对象创建时指定的基因ID。
参数：level
An integer giving the level of the chromosome band tree at which testing should begin. The level is conceptualized as the set of nodes with a given path length to the root (organism) node of the chromosome band tree. So level 1 is the chromosome and level 2 is the chromosome arms. You can get a better sense by calling exampleLevels(chrtree)
一个整数，在测试的染色体带树的水平应该开始。水平概念化为一个给定的路径长度根（生物）染色体带树节点的节点集。因此，第1级是染色体和第2级是染色体武器。你可以通过调用exampleLevels(chrtree)一个更好的感觉
参数：dir
A string giving the direction in which the chromosome band tree will be traversed when carrying out the tests. A bottom up traversal, from leaves to root, is specified by "up". A top down, from root to leaves, traversal is specified by "down".
一个字符串，给出在染色体带树将进行测试时，走过的方向。长达遍历底部，从叶到根指定"up"的。自上而下，从根到叶，遍历指定"down"。
参数：type
A string giving the type of test to perform. The current choices are "local" and "global". A local test carries out a chisq.test on each 2 x K contingency table induced by each set of siblings at a given level in the tree. A global test uses the Hypergeometric distribution to compute a p-value for the 2 x 2 tables induced by each band treated independently.
字符串执行的测试类型。目前的选择是"local"和"global"。一个地方进行测试chisq.test上每2 X的k应变诱导每一组的兄弟姐妹在树中的一个给定级别的表。一个全球性的测试使用超几何分布计算为2×2独立处理每个波段的诱导表的p值。
参数：next.pval
The p-value cutoff used to determine whether the parents or children of a node should be tested. After testing a given level of the tree, the decision of whether or not to continue testing the children (or parents) of the already tested nodes is made by comparing the p-value result for a given node with this cutoff; relatives of nodes with values strictly greater than the cutoff are skipped.
p值截止使用，以确定是否应测试一个节点的孩子的父母或。树的水平测试后，决定是否继续测试已经测试节点的孩子（或父母）是由比较p值的结果与此截止节点;节点亲属严格大于截止值被跳过。
参数：cond.pval
The p-value cutoff used to determine whether a node is significant during a conditional test. See conditional.
p值截止用来确定一个节点是否是有条件的测试过程中具有重要意义。看到conditional。
参数：conditional
A logical value. Can only be used when dir="up" and type="global". In this case, a TRUE value causes a conditional Hypergeometric calculation to be performed. The genes annotated at significant children of a given band are removed before testing.
一个逻辑值。只能当dir="up"和type="global"。在这种情况下，一个TRUE值导致进行有条件的超几何计算。显著儿童在一个给定的带注释的基因测试前被删除。
值----------Value----------
A list with an element for each level of the tree that was tested. Note that the first element will correspond to the level given by level and that subsequent elements will be the next or previous depending on dir.
测试树的每个级别的元素列表。请注意，第一个元素对应到level水平和后续元素上dir取决于下一个或上一个。
Each level element is itself a list consisting of a result list for each node or set of nodes tested. These inner-most lists will have, at least, the following components:
每个级别的元素，本身就是一个结果列表中的每个节点或测试节点集组成的一个列表。大多数这些内在名单，至少将有以下组件：
参数：nodes
A character vector of the nodes involved in the test.
在测试中所涉及的节点的一个特征向量。
参数：p.value
The p-value for the test
p值的测试
参数：observed
The contingency table
应急表
参数：method
A brief description of the test method
一个测试方法的简要说明
作者（S）----------Author(s)----------
Seth Falcon
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 14:06:31
