generateSeeds-methods(rqubic)
generateSeeds-methods()所属R语言包：rqubic
Generate seeds for biclustering
生成双聚类种子
译者：生物统计家园网 机器人LoveR
描述----------Description----------
generateSeeds takes either matrix or an ExpressionSet object to generate seeds. Seeds are defined as pairs of genes (edges) which share coincident expression levels in samples. The higher the coincidence, the higher the score of the seeds will be. The seeds are generated by subsequent comparing each pair of genes. When all seeds have been produced, they are sorted by the coincidence scores and returned as an object. See the details section for notes on implementation.
generateSeeds无论是矩阵或ExpressionSet对象生成种子。种子被定义为对共享样品中一致表达水平的基因（边）。较高的巧合，得分较高的种子会。随后比较每对基因产生的种子。当所有的种子已经产生，他们是由巧合成绩排序，并作为对象返回。执引号况的说明，请参阅详细信息部分。
方法----------Methods----------
In the rqubic package, generateSeeds currently supports two data types: ExpressionSet (an inherited type of eSet, or numeric matrix.
rqubic包generateSeeds目前支持两种类型的数据：ExpressionSet（eSet继承类型，或数字矩阵。
Both methods requires in addition a parameter, minColWidth, specifying the minimum number of conditions shared by the two genes of each seed. Its default value is 2. When this default value is used, the minimum coincidence score is defined as max(2, ncol/20), where ncol represents the number of conditions. When a non-default value is provided, the value is used to select seeds.
这两种方法都需要在另外一个参数，minColWidth，指定每个种子的两个基因共同条件的最低数量。其默认值是2。当使用此默认值，最小的巧合得分被定义为max(2, ncol/20)，ncol代表的一些条件。当一个非默认值，该值用于选择种子。
signature(object = "eSet") An object representing expression data. Note that the exprs must be a matrix of integers, otherwise the method warns and coerces the storage mode
signature(object = "eSet")代表表达数据对象。请注意，exprs必须是整数矩阵，否则该方法警告和胁迫的存储模式
signature(object = "matrix") A matrix of integers. In case filled by non-integers, the method warns and coerces the storage mode
signature(object = "matrix")一个整数矩阵。在充满非整数的情况下，该方法警告和胁迫的存储模式
Details
详情----------Details----------
The function compares all pairs of genes, namely all edges of a complete graph composed by genes. The weight of each edge is defined as the number of samples, in which two genes have the same expression level. This weight, also known as the coincidence score, reflects the co-regulation relationship between two genes.
功能比较所有对基因，即由基因组成一个完整的图形的所有边。每边的重量被定义为样品的数量，这两个基因具有相同的表达水平。这个重量，也称为巧合的得分，反映了两个基因之间的监管合作关系。
The seed is chosen by picking edges with higher scores than the minimum score, provided by the minColWidth parameter (default: 2).
种子选择采摘边缘具有更高的分数比最低分数minColWidth参数（默认是：2）提供的。
To implement such a selection algorithm, a Fibonacci heap is constructed in the C codes. Its size is predefined as a constant, which should be reduced in case the gene number is too large to run the algorithm. A new seed, which was selected by having a higher coincidence score than the minimum, is inserted to the heap. And dependent on whether the heap is full or not, it is either inserted by squeezing the minimum seed out, or put into the heap directly.
为了实现这样的选择算法，Fibonacci堆建在C代码。它的大小是一个常数预定义，应减少的情况下，基因数目太大，运行算法。一个新的种子，这是有巧合得分高于最低的选择，插入到堆。和堆是否是完整或不依赖，它被挤压最低种子插入，或直接把堆。
Once the heap is filled by examining all pairs of genes, it is dumped into an array of edge pointers, with decreasingly ordered edge pointers by their scores. This array is captured as an external pointer, attached as an attribute of an rqubicSeeds object.
一旦通过检查所有对基因填补堆，它倒进一个边缘指针数组，他们的分数少地下令边缘指针。作为一个外部的指针，作为一个rqubicSeeds对象的属性附加，这个数组被捕获。
An rqubicSeeds object holds an integer, which records the height of the heap. It has (besides the class identifier) two attributes: one for the external pointer, and the other one for the threshold of the coincidence score.
rqubicSeeds对象持有一个整数，它记录堆的高度。它（除了类标识符）两个属性：一个外部指针，和另外一个的巧合得分的阈值。
注意----------Note----------
In the rqubic implementation, the variable arr_c[i][j] holds the level symbols (-1, 0, 1 in the default case), whereas in the QUBIC implementation, this variable holds the index of level symbols, and the level symbols are saved in the global variable symbols.
在rqubic执行，变量arr_c[i][j]持有水平符号（-1, 0, 1在默认情况下），而在QUBIC实施，这个变量保存水平指数符号，水平符号被保存在全局变量symbols。
作者（S）----------Author(s)----------
Jitao David Zhang <jitao_david.zhang@roche.com>
举例----------Examples----------
data(sample.ExpressionSet, package="Biobase")
sample.disc <- quantileDiscretize(sample.ExpressionSet)
sample.seeds <- generateSeeds(sample.disc)
sample.seeds
## with higher threshold of incidence score[＃具有较高的发病率得分的阈值]
sample.seeds.higher <- generateSeeds(sample.disc, minColWidth=5)
sample.seeds.higher
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 13:27:00
