equivalentGOProfiles(goProfiles)
equivalentGOProfiles()所属R语言包：goProfiles
Are two lists of genes equivalent in terms of their Gene Ontology profiles?
两个基因，相当于基因本体型材名单吗？
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs an equivalence test based on the squared Euclidean distance between the Gene Ontology profiles of two lists of genes. Equivalence is declared if the upper limit d.sup of a one-sided confidence interval [0, d.sup] for the distance is lesser than the equivalence limit d0.
执行基于基因本体型材之间的两个基因名单上的平方欧氏距离的等价测试。等价宣布，如果一种片面的置信区间的上限d.sup [0，d.sup距离比等价的限制D0较小。
用法----------Usage----------
equivalentGOProfiles(goObject, ...)
## S3 method for class 'GOProfileHtest'
equivalentGOProfiles(goObject, equivEpsilon = 0.05, d0 = NULL, confidence = NULL, ...)
## S3 method for class 'list'
equivalentGOProfiles(goObject, ...)
## S3 method for class 'ExpandedGOProfile'
equivalentGOProfiles(goObject, qm=NULL, pqn0=NULL,
n = ngenes(goObject), m = ngenes(qm), n0 = ngenes(pqn0),
confidence = 0.95,
equivEpsilon = 0.05, d0 = NULL,
simplify = FALSE, ...)
## Default S3 method:[默认方法]
equivalentGOProfiles(goObject, ...)
参数----------Arguments----------
参数：goObject
an object related to GO profiles or comparisons between them
去型材或比较它们之间的相关对象
参数：qm
an expanded GO profile, i.e. and object of class 'ExpandedGOProfile'
扩大的好配置文件，即对象类的ExpandedGOProfile
参数：pqn0
an expanded GO profile, i.e. and object of class 'ExpandedGOProfile'
扩大的好配置文件，即对象类的ExpandedGOProfile
参数：n
a numeric vector with the number of genes profiled in each column of goObject. This parameter is included to allow the possibility of exploring the consequences of varying sample sizes, other than the true sample size in goObject.
在每列goObject异形基因的数量与数字向量。此参数包括允许探索不同的样本大小，比在goObject的真正的样本大小的后果的可能性。
参数：m
a numeric vector with the number of genes profiled in each column of qm.
数值向量与QM列在每个异形基因的数量的。
参数：n0
a numeric vector with the number of genes profiled in each column of pqn0.
在每列pqn0异形的基因数量与数字向量。
参数：confidence
the nominal confidence level of the one-sided confidence interval on the distance
片面的置信区间距离的名义置信水平
参数：d0
a positive value specifying the equivalence limit
正值指定等价限制
参数：equivEpsilon
a positive value used to compute 'd0' if it is not directly available
正值用于计算D0，如果它不是直接可用
参数：simplify
should the result be simplified, if possible? See the 'Details' section
结果应予以简化，如果可能的话吗？见“详细资料”一节
参数：...
further arguments, tipically the same than to 'compareGOProfiles'
进一步的论据，tipically比“compareGOProfiles
Details
详情----------Details----------
An object of S3 class "ExpandedGOProfile" is, essentially, a "data.frame" object with each column representing the relative frequencies in all observed node combinations, resulting from profiling a set of genes, for a given and fixed ontology. The 'row.names' attribute codifies the node combinations and each "data.frame" column (say, each profile) has an attribute, 'ngenes', indicating the number of profiled genes.
S3类“ExpandedGOProfile”的对象，基本上是一个“数据框”代表所有观测到的节点组合的相对频率，造成一组基因分析某一固定的本体各列的对象。 “row.names”属性编纂节点的组合，每列“数据框”（例如，每个配置文件）的属性，ngenes“，说明了异形的基因数量。
In the 'ExpandedGOProfile' interface, the arguments 'goObject', 'qm' and 'pqn0' are compared in a column by column wise, recycling columns, if necessary, in order to perform max(ncol(goObject),ncol(qm),ncol(pqn0)) equivalence tests (each test resulting in an object of class 'htest'). In order to be properly tested, these arguments are expanded by row, according to their row names. That is, the data arguments can have unequal row numbers. Then, they are expanded adding rows with zero frequencies, in order to make them comparable. In the i-th comparison (i from 1 to max(ncol(goObject),ncol(qm),ncol(pqn0))), the parameters n, m and n0 are included to allow the possibility of exploring the consequences of varying sample sizes, other than the true sample sizes included as an attribute in goObject, qm and pqn0. When qm = NULL, the genes profiled in goObject are compared with a subsample of them, those profiled in pqn0 (is there equivalence between a set of genes and a restricted subset, e.g. those overexpressed under a disease, in terms of their profiles?). When pqn0 = NULL, an equivalence test between two profiles with no genes in common is performed.
在“ExpandedGOProfile”界面，参数“goObject，QM和pqn0比较明智列在一列，回收列，如果有必要，为了执行最大（NCOL（goObject），NCOL（QM） ，NCOL（pqn0））等价测试（每个测试对象类的htest“）。以正确的测试，这些参数由行扩大，根据他们的行名。也就是说，数据参数可以有不平等的行号。然后，他们扩大零频率增加的行，以使他们可比。 （我在第i个比较从1到最大（NCOL（goObject），NCOL（QM），NCOL（pqn0））），参数N，M和N0包括允许探索不同样本的后果的可能性大小，比真正的样品作为在goObject，QM和pqn0的属性包括大小等。 QM = NULL时，异形在goObject的基因与他们的子样本，pqn0异形相比（有一组基因和受限制的子集之间的等价下的疾病，如那些过度表达他们的个人资料？） 。当pqn0 = NULL，两个没有共同的基因型材之间的等价测试执行。
In the 'GOProfileHtest' interface, the one-sided confidence interval for the squared Euclidean distance is computed from the distance and its standard error stored in the corresponding fields of the argument goObject, itself typically an object of class 'GOProfileHtest' resulting from a call to 'compareGOProfiles' with simplify=T.
在“GOProfileHtest”界面，片面的置信区间平方欧几里德距离计算的距离和存储在相应的的说法goObject的领域，其标准错误，本身通常是一个类的GOProfileHtest“从通话对象compareGOProfiles简化= T
In the 'list' interface, the argument goObject is intended to be a list of objects of class 'GOProfileHtest' typically resulting from a call to 'compareGOProfiles' with simplify=F. The call to the method is iterated along the list, and the one-sided confidence interval for the squared Euclidean distance is computed from the distance and its standard error stored in the corresponding fields of all the members of the list.
在“列表”界面，参数goObject旨在成为一个类的GOProfileHtest“的对象名单，通常从一个调用”compareGOProfiles简化= F方法调用迭代沿着列表，从列表中的所有成员的相应字段中存储的距离和标准错误和片面的置信区间为平方欧氏距离计算。
In the default interface, the 'goObject' argument is previously converted into an object of class 'ExpandedGOProfile' and then this interface is used.
在默认的界面，以前的“goObject的说法转换成类的ExpandedGOProfile”，然后使用此接口的对象。
If the argument 'd0' is not provided it is computed as d0 <- s * equivEpsilon^2, where 's' stands for the number of non empty GO nodes in any of the GO profiles being compared.
如果没有提供的参数D0d0 <- s * equivEpsilon^2，S代表被比较好型材的任何非空的好节点数量计算。
值----------Value----------
In the 'ExpandedGOProfile' and 'list' interfaces, the result is a list of objects of class "htest" or a single "htest" object if there is only one object in the list and simplify == T. In the other interfaces, the result is a single "htest" object. Each one of these "htest" objects has the following fields:
在“ExpandedGOProfile”和“列表”界面，其结果是类的“htest”或一个“htest”对象的对象列表，如果只有一个对象列表，并简化了在其他==吨接口，其结果是一个单一的“htest”的对象。这些“htest”对象中的每一个具有以下字段：
参数：statistic
test statistic, (distance - d0) / se
测试统计，（距离 - D0）/ SE
参数：parameter
d0 and the sample sizes (number of genes) n and m
D0和样品尺寸（基因数）n和m
参数：p.value
associated p-value to test the null hypothesis of profiles inequivalence
相关的p值测试型材不对称性的零假设
参数：conf.int
asymptotic one-sided confidence interval for the squared euclidean distance. Its attribute "conf.level" contains its nominal confidence level.
片面平方欧几里德距离渐近置信区间。其属性“conf.level”包含其标称的信心水平。
参数：estimate
squared euclidean distance between the contracted profiles. Its attribute "se" contains its standard error estimate
承包模式之间的欧氏距离平方。 “SE”其属性包含其标准误差估计
参数：data.name
a character string giving the names of the data
提供的数据的名称字符串
参数：alternative
a character string describing the alternative hypothesis (always 'Equivalence or similarity, true squared Euclidean distance between the contracted profiles is less than d0'
字符串描述替代假说（总是等值或相似的，真正的承包模式之间的欧几里德距离平方比D0少“
作者（S）----------Author(s)----------
Jordi Ocana
参见----------See Also----------
'compareGOProfiles'
“compareGOProfiles”
举例----------Examples----------
data(prostateIds)
expandedWelsh <- expandedProfile(welsh01EntrezIDs[1:100], onto="MF",
level=2, orgPackage="org.Hs.eg.db")
expandedSingh <- expandedProfile(singh01EntrezIDs[1:100], onto="MF",
level=2, orgPackage="org.Hs.eg.db")
commonGenes <- intersect(welsh01EntrezIDs[1:100], singh01EntrezIDs[1:100])
commonExpanded <- expandedProfile(commonGenes, onto="MF", level=2, orgPackage="org.Hs.eg.db")
equivMF <-equivalentGOProfiles (expandedWelsh[['MF']],
qm = expandedSingh[['MF']],
pqn0= commonExpanded[['MF']])
print(equivSummary(equivMF, decs=5))
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。
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发表于 2012-2-25 20:48:54
