SpeCond(SpeCond)
SpeCond()所属R语言包：SpeCond
The condition-specific detection function
在特定条件的检测功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
SpeCond performs a full condition-specific detection from an expression matrix
SpeCond执行从表达矩阵的充分条件，具体检测
用法----------Usage----------
SpeCond(expressionMatrix, param.detection = NULL,
multitest.correction.method = "BY", prefix.file = "A",
print.hist.pv = FALSE, fit1 = NULL, fit2 = NULL,
specificOutlierStep1 = NULL, condition.factor=NULL,
condition.method=c("mean","max"))
参数----------Arguments----------
参数：expressionMatrix
an ExpressionSet object or a matrix of expression values (in log2); columns are the conditions, rows are genes (or probe sets)
一个ExpressionSet对象或一个表达式的值矩阵（以log2）;列的条件下，行基因（或探针组）
参数：param.detection
the parameter matrix for the detection must contain the values for "lambda", "beta", "per", "md", "mlk" ,"rsd' and "pv" for the two steps of the procedure. Can be obtained by getDefaultParameter or createParameterMatrix
检测参数矩阵必须包含两个步骤“拉姆达”，“试用”，“每”，“MD”，“MLK”，“区署”，“PV”的价值观的过程。可以得到getDefaultParameter或createParameterMatrix
参数：multitest.correction.method
the multitest correction method. The default is "BY", for the possible values see p.adjust
了Multitest的校正方法。默认是“”，为可能的值看到p.adjust
参数：prefix.file
a prefix added to the histogram file (if produced). It will be used to link to the result html pages generated by other functions using the result object of this function (if no other prefix value is implemented). The default is "A". It is useful to change the prefix when you perform a new analysis with different parameters as you may want to compare the results
前缀添加到直方图的文件（如生产）。它将被用于链接到其他功能，使用此功能的结果对象（如果没有其他的前缀值实现）所产生的结果HTML页面。默认是“A”。它是有用的改变前缀，当您执行一个新的分析，用不同的参数，你可能要比较的结果
参数：print.hist.pv
a logical (TRUE/FALSE) value indicating whether a histogram of (non-adjusted) p-values is to be printed; the default is FALSE
逻辑（真/假）值，该值指示是否直方图（非调整）p值是要打印，默认为FALSE
参数：fit1
the result of fitPrior containing the parameter of the mixture normal model of the expression data. If NULL fitPrior function will be called
fitPrior含有正常表达数据的混合模型参数的结果。如果为NULLfitPrior函数将被调用
参数：fit2
the result of fitNoPriorWithExclusion containing the parameter of the mixture normal model of the expression data ignoring the outliers detected in the first step of the procedure. If NULL, fitNoPriorWithExclusion function will be called
fitNoPriorWithExclusion含有正常的表达，忽略了在该过程的第一步检测的离群数据的混合模型参数的结果。如果为NULL，fitNoPriorWithExclusion函数将被调用
参数：specificOutlierStep1
the list of outliers detected by the first step procedure, result of the getSpecificOtuliersStep1 function. If NULL, getSpecifcOutliersSpep1 will be called
检测离群的第一步程序，getSpecificOtuliersStep1函数的结果列表。如果为NULL，getSpecifcOutliersSpep1会被称为
参数：condition.factor
this argument can be used if expressionMatrix is an ExpressionSet object; a factor object of length equal to the number of columns (samples) of the ExpressionSet object specifying which sample(s) belong to which condition (condition.factor levels); can be extracted from the phenoData
如果这种说法，可以使用的expressionMatrix是ExpressionSet对象;长度等于列数（样品）样品（S）属于哪个条件（condition.factor水平）指定的ExpressionSet对象的因素对象可以提取;在phenoData
参数：condition.method
this argument can be used if expressionMatrix is an ExpressionSet object; the method (mean or max) to summarise the samples by conditions (defined by the condition.factor vector)
这种说法，可以被用来，如果expressionMatrix是ExpressionSet对象;的方法（或最大）总结样本条件（定义由condition.factor向量）
Details
详情----------Details----------
SpeCond uses the Mclust function to obtain the mixture of normal distributions uses by the detection procedure.
SpeCond使用Mclust函数获得混合正态分布的检测程序使用。
If expressionMatrix is an ExpressionSet object it is necessary to obtain an expression value matrix. This is obtain by the getMatrixFromExpressionSet function. This take into consideration if condition.factor is not NULL the transformation of the expression values for the several samples of each condition to one expression values for each condition for each gene.
如果expressionMatrix是ExpressionSet的对象是要获得一个表达式的值矩阵。这是获得getMatrixFromExpressionSet功能。这考虑到如果condition.factor不是NULL改造的几个样品中每个条件的每一个基因的每个条件表达式的值的表达式的值。
If print.hist.pv is TRUE the histogramme of the non-adjusted p-values is plotted. It is a way to check the normal distribution fitting. If the histogramme is relatively flat the normal distribution(s) fits properly the data.
如果print.hist.pv是TRUE，非调整p值histogramme绘制。它是一种方法来检查正态分布拟合。 ，如果histogramme是相对平坦的正态分布（S）恰当的数据。
值----------Value----------
An object of class sp_list
一个对象的类sp_list
参数：prefix.file
the prefix used for this analysis. It will be used by default in the function getFullHtmlSpeCondResult and getGeneHtmlPage
用于此分析的前缀。默认情况下，它将被用来在函数getFullHtmlSpeCondResult和getGeneHtmlPage
参数：fit1
the fitting parameters used by the detection in the first step of the procedure: the result of the fitPrior function called internally or the same as the fit1 argument if not NULL
用于检测程序的第一步：fitPrior内部调用的函数或相同的为FIT1参数的，如果不为NULL结果的拟合参数
参数：fit2
the fitting parameters used by the detection in the second step of the procedure: the result of the fitNoPriorWithExclusion function called internally or the same as the fit2 argument if not NULL
在检测过程的第二个步骤所使用的拟合参数：fitNoPriorWithExclusion内部调用的函数作为的FIT2参数相同，如果不为NULL的结果
参数：specificOutliersStep1
the condition(s) for which the expression value of the gene is detected as outlier in the first step of the procedure. If NULL, no expression value has been detected in the first step. The second fitting ignores these expression values
条件（S）的基因表达程序的第一步离群值检测。如果为NULL，没有表达的价值已经被检测的第一步。第二件忽略这些表达式的值
参数：specificResult
a list of 7 attributes containing al the specific results. This object result of getSpecificResult
7属性包含人的具体结果列表。这种getSpecificResult的对象结果
作者（S）----------Author(s)----------
Florence Cavalli, florence@ebi.ac.uk
参考文献----------References----------
Journal of the American Statistical Association, Vol. 97, pages 611-631 (2002).
Technical Report No. 504, Department of Statistics, University of Washington, September 2006.
参见----------See Also----------
Mclust, fitPrior, fitNoPriorwithExclusion,
Mclust，fitPrior，fitNoPriorwithExclusion
举例----------Examples----------
library(SpeCond)
data(expressionSpeCondExample)
dim(expressionSpeCondExample)
##Perform the condition specific detection analysis with SpeCond()[＃执行的具体检测分析与SpeCond条件（）]
generalResult=SpeCond(expressionSpeCondExample, param.detection=NULL,
multitest.correction.method="BY", prefix.file="E", print.hist.pv=TRUE,
fit1=NULL, fit2=NULL, specificOutlierStep1=NULL)
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 2012-2-26 14:51:43
