contractedProfile(goProfiles)
contractedProfile()所属R语言包：goProfiles
Converts an expanded GO profile into a basic (contracted) GO profile
一个基本的（合同）GO资料转换成扩大围棋剖面
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Converts an object of class 'ExpandedGOProfile', or assimilable to it, in an object of class 'BasicGOProfile'
转换类的ExpandedGOProfile，或同化它的对象，在类的BasicGOProfile“的对象
用法----------Usage----------
contractedProfile(prof, nams = NULL)
## S3 method for class 'ExpandedGOProfile'
contractedProfile(prof, nams = NULL)
## Default S3 method:[默认方法]
contractedProfile(prof, nams = NULL)
参数----------Arguments----------
参数：prof
an expanded GO profile, i.e. and object of class 'ExpandedGOProfile', or a numeric vector assimilable to an expanded profile, see the "details" section
扩大围棋的文件，即类的ExpandedGOProfile“，或数字向量，以扩大个人资料同化的对象，看到的”细节“一节
参数：nams
optionally, the names of the annotated combinations of GO nodes whose frequency is represented in the expanded profile, see the "details" section
选择性好节点，其频率扩大姿态表示的注解组合的名字，看到的“细节”一节
Details
详情----------Details----------
Given a list of n genes, and a set of s GO nodes X, Y, Z, ... in a given ontology (BP, MF or CC), its associated (contracted) "profile" is the frequencies vector (either absolute or relative frequencies) of annotations or hits of the n genes in each node. For a given node, say X, this frequency includes all annotations for X alone, for X and Y, for X and Z and so on. Thus, as relative frequencies, its sum is not necessarily one, or as absolute frequencies their sum is not necessarily n. Basic contracted profiles are represented by objects of S3 class 'BasicGOProfile'. On the other hand, an "expanded profile" corresponds to the frequencies in ALL OBSERVED NODE COMBINATIONS. That is, if n genes have been profiled, the expanded profile stands for the frequency of all hits EXCLUSIVELY in nodes X, Y, Z, ..., jointly with all hits simultaneously in nodes X and Y (and only in X and Y), simultaneously in X and Z, in Y and Z, ... , in X and Y and Z (and only in X,Y,Z), and so on. Thus, their sum is one. Expanded profiles are represented by objects of S3 class 'ExpandedGOProfile'. The generic function 'contractedProfile' "contracts" an expanded profile, either represented by a 'ExpandedGOProfile' object or a numeric vector interpretable as an expanded profile, in order to obtain its contracted profile representation.
给定一个N基因的列表，和一组s的节点X，Y，Z轴，...在一个给定的本体（BP，MF或CC），及其相关的（合同）“个人资料”是在每个节点上的N基因的注解或命中（绝对或相对频率）的频率向量。对于一个给定节点，说X，这个频率包括所有注释为X，X和Y单，X和Z等。因此，相对频率，其总和未必，或它们的总和，为绝对频率不一定是n个。合同基本配置文件代表S3类的BasicGOProfile“的对象。另一方面，“扩大个人”对应的频率在所有观察节点组合。也就是说，如果n基因已被异形，扩大轮廓代表所有点击的频率只在节点X，Y，Z轴，...，共同所有命中同时节点X和Y（仅在X和Y ），同时在X和Z，Y和Z，...在X和Y和Z（只有在X，Y，Z轴），等等。因此，他们的总和就是其中之一。扩大型材为代表的S3类的ExpandedGOProfile“的对象。 “合同”通用功能“contractedProfile扩大的个人资料，无论是代表”ExpandedGOProfile对象或一个数值向量作为扩大剖面解释，以取得其承包的文件表示。
The rownames attribute of an 'ExpandedGOProfile' or, equivalently, the names attribute of a vector representing an expanded profile, or the nams argument, must represent the GO nodes combinations separating the node names with dots, ".", for example: "X", "Y", "Z", "X.Y", "X.Z", "Y.Z", "X.Y.Z" and so on.
rownames属性ExpandedGOProfile或等价地，names属性向量代表一个扩大的个人资料，或nams参数，必须代表GO节点组合分离的节点名称点，例如，“。”的“X”，“Y”，“Z”，“X.Y”，“X.Z”，“Y.Z”，“某某“等。
值----------Value----------
An object of class 'BasicGOProfile' the contracted profile representation of the
一个对象类的BasicGOProfile“的合同的文件表示
作者（S）----------Author(s)----------
Jordi Ocana
举例----------Examples----------
data(prostateIds)
expandedWelsh <- expandedProfile(welsh01EntrezIDs[1:100], onto="MF",
level=2, orgPackage="org.Hs.eg.db")
reContractedWelsh <- contractedProfile(expandedWelsh[["MF"]])
print(expandedWelsh)
print(reContractedWelsh)
class(reContractedWelsh)
ngenes(reContractedWelsh)
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 20:48:31
