R语言 SpeCond包 createParameterMatrix()函数中文帮助文档(中英文对照)

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createParameterMatrix(SpeCond)
createParameterMatrix()所属R语言包：SpeCond

                                         Create or Modify the SpeCond argument parameters
                                         创建或修改的SpeCond参数参数

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

createParameterMatrix creates and/or modifies the param.detection matrix used as argument in the SpeCond function. If parm.detection is NULL the param.detection matrix used is the one containing the default parameter values, as obtained by getDefaultParameter. The remaining arguments enable to change the values of the param.detection matrix.
createParameterMatrix创建和/或，修改param.detection矩阵作为参数使用在SpeCond功能。如果parm.detection是NULL使用的param.detection基质是一个包含默认参数值，如获得通过getDefaultParameter。其余的参数使改变的param.detection矩阵值。


用法----------Usage----------


createParameterMatrix(param.detection = NULL, beta.1 = NULL, beta.2 = NULL,
lambda.1 = NULL, lambda.2 = NULL, per.1 = NULL, per.2 = NULL, md.1 = NULL,
md.2 = NULL, mlk.1 = NULL, mlk.2 = NULL, rsd.1 = NULL, rsd.2 = NULL,
pv.1 = NULL, pv.2 = NULL)



参数----------Arguments----------

参数：param.detection
a matrix of 2 rows and 7 columns as the result of getDefaultParameter
作为2行和第7列的矩阵的getDefaultParameter结果


参数：beta.1
Influences the prior applied during the determination of the variance of the normal distributions. It is necessary in the first fitting step to allow the model to capture isolated outliers.
在正态分布的方差的决心影响事先申请。这是必要的，在装修第一步骤，以使模型捕捉孤立离群。


参数：beta.2
The normal use of SpeCond does not prior on Step2: must be set to 0
正常使用的SpeCond不事先对第二步：必须设置为0


参数：lambda.1
Influences the choice of models by affecting the selection of one, two or three normal distributions, thus introducing some weight on the effect of number of parameters to be defined. The default is 1, the model uses the BIC value taking into account the log-likelihood value.  
影响模式的选择，影响选择一个，两个或三个正态分布效果被定义的参数的数量，从而引入一些体重。默认值是1，该模型使用的BIC值，考虑到对数似然值。


参数：lambda.2
Same as lambda.1 for the second step of the SpeCond function
同为lambda.1的的SpeCond功能的第二个步骤


参数：per.1
percentage threshold: this is the percentage of conditions that can be detected as specific. As per increases a larger number of expression values per genes can be identified as specific. The default is 0.1
阈值百分比：这是可以作为特定检测条件的百分比。每增加较大数量的每个基因的表达值可以具体确定。默认的是0.1


参数：per.2
percentage threshold: This is the final percentage of condition that can be detected as specific. As per increases a larger number of expression values per genes can be identified as specific. The default is 0.3
阈值百分比：这是最后的百分比，可作为特定检测条件。每增加较大数量的每个基因的表达值可以具体确定。默认的是0.3


参数：md.1
  median difference: this is the minimum value between the median values of two mixture components that is allowed to identify one of them as representing outliers, i.e. possibly not part of the null distribution. This corresponds to a biological fact; specific expression that corresponds to noise should not be detected as specific
中位数的区别：这是两种混合组件允许以确定其中的一个代表离群，即可能不空分布的中值之间的最低值。这相当于生物的事实;对应噪声的具体体现，不应被视为特定的检测


参数：md.2
Same as md.1 for the second step of the SpeCond function. For consistency should be equal to md.1
相同md.1第二步的SpeCond功能。对于一致性应该是平等的md.1


参数：mlk.1
minimum log-likelihood: enables the identification of clusters of conditions that are well separated from the others in the model. If the gene mlk value>mlk, the mixture component can be detected as outlier (i.e. not part of the null distribution)
最小log的可能性：使聚类条件，以及从其他模型中分离鉴定。 > MLK如果MLK价值的基因，混合组件可以检测作为离群值（即不空分布的一部分）


参数：mlk.2
same as mlk.2 for the second step of the SpeCond function
同为mlk.2的的SpeCond功能的第二个步骤


参数：rsd.1
minimum of standard deviation ratio: enables the identification of clusters of conditions that are extremely spread out compared to the distribution clustering of most expression values. If the gene rsd values< rsd the mixture component can be detected as outlier (i.e. not part of the null distribution)
最低标准差比：使条件非常摊开相比，大多数表达式的值分布聚类簇的鉴定。如果基因<RSD值RSD为混合成分可以检测离群值（即不空分布的一部分）


参数：rsd.2
same as rsd.1 for the second step of the SpeCond function
同为rsd.1的的SpeCond功能的第二个步骤


参数：pv.1
p-value threshold to detect a condition as specific for a given gene
p值阈值来检测一个特定基因的具体条件


参数：pv.2
same as pv.1 for the second step of the SpeCond function, for consistency should be equal to pv.1
一样pv.1为第二步的SpeCond功能，一致性应该等于pv.1


值----------Value----------

param.detection: a matrix of 2 row and 7 columns. The rows "Step1 "and "Step2" correspond respectively to the first and second set of parameters for the SpeCond function. The parameters (columns) are: lambda, beta, per, md, mlk, rsd. See the createParameterMatrix documentation for more details about the parameters.
param.detection：2行7列的矩阵。行的“第一步”和“第二步”，分别对应于第一和第二组为SpeCond功能参数。参数（列）：λ，β，每医师，MLK，RSD。见createParameterMatrix文件的有关参数的更多细节。


警告----------Warning----------

The SpeCond code is based on: beta.2=0 md.1=md.2 per.1<=per.2 pv.1=pv.2
SpeCond代码是基于：beta.2 = 0 md.1 = md.2 per.1 <= per.2 pv.1 = pv.2


作者（S）----------Author(s)----------


Florence Cavalli, florence@ebi.ac.uk



参见----------See Also----------

getDefaultParameter
getDefaultParameter


举例----------Examples----------


##Get the default parameters and changing the mlk.1 value to 10:[＃获取默认参数和改变mlk.1价值10：]
param.detection2=createParameterMatrix(mlk.1=10)
param.detection2
## Modify param.detection2 with mlk.1 value to 15 and rsd.2 value to 0.2[＃修改param.detection2的的mlk.1价值15和rsd.2价值0.2]
param.detection2B=createParameterMatrix(param.detection=param.detection2,
mlk.1=10, rsd.2=0.2)
param.detection2B

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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