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

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BASHCompact(beadarray)
BASHCompact()所属R语言包：beadarray

                                        BASH - Compact Defect Analysis
                                          - 紧凑型的BASH的缺陷分析

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Creates a list of probes marked as being in compact defects.
创建一个标记探针在紧凑的缺陷列表。


用法----------Usage----------


BASHCompact(inten, probeIDs, neighbours = NULL, wts=1, n=3, maxiter = 10, cutoff = 8,  cinvasions = 10, outlierFun=illuminaOutlierMethod, ...)



参数----------Arguments----------

参数：inten
the (transformed) intensities associated with beads on an array.
（转换）与数组珠相关的强度。


参数：probeIDs
the probe identities associated with those beads (i.e. indicating which beads are of which sort)
那些珠子探针关联的身份（即珠是其中排序）


参数：neighbours
A Neighbours matrix such as that generated by generateNeighbours. Compulsory - the function will no longer generate this for you.
如generateNeighbours生成的邻居矩阵。强制 - 的功能将不再为您生成这个。


参数：wts
weights indicating any beads to be masked in calculations.
指示在计算任何屏蔽珠的重量。


参数：n
Specify a cut-off for outliers (e.g. as n median absolute deviations (MADs) from the median). The default value is 3
指定为离群值（例如列印绝对偏差的中位数，中位数（MADS））截止。默认值是3


参数：maxiter
Integer - Maximum number of iterations.
整数 - 最大迭代次数。


参数：cutoff
Integer - Size a cluster must be to be labelled a compact defect.
整数 - 大小的聚类必须被贴上一个紧凑的缺陷。


参数：cinvasions
Integer - Number of invasions used when closing the image.
整数 - 关闭图像时使用的入侵。


参数：outlierFun
the choice of outlier calling function to use.
在选择离群通话功能使用。


参数：...
Additional arguments to be passed to outmeth.
额外的参数被传递到outmeth。


Details

详情----------Details----------

BASHCompact finds "compact defects" on an array. A compact defect is defined as a large connected cluster of outliers.
BASHCompact发现一个阵列上的“紧凑型缺陷”。大连接离聚类群被定义为一个紧凑的缺陷。

This function first finds the outliers on an array. This is done via the user's choice of function (e.g. illuminaOutlierMethod or squeezedVarOutlierMethod.
这个函数首先发现阵列上的离群。这是通过用户的选择功能（例如illuminaOutlierMethod或squeezedVarOutlierMethod。

Next, using the Neighbours matrix and a Flood Fill algorithm, it determines which beads are in large connected clusters of outliers (of size larger than cutoff). These beads are then temporarily removed and the process repeated with the remaining beads. The repetition continues until either no large clusters of outliers remain, or until we have repeated the process maxiter times (and in this case, a warning will be given). In this way, we obtain a list of defective probes.
接下来，使用邻居矩阵和洪水填充算法，它决定哪些珠大连接聚类离群（大小比cutoff）。这些珠子，然后暂时删除，其余珠反复的过程。重复继续，直到仍然没有大型聚类离群，或maxiter倍（在这种情况下，将给予警告），直到我们反复的过程。这样，我们得到了一个有缺陷的探针。

Finally, we "close" the image, to fill in small gaps in the defect image. This consists of a "dilation" and an "erosion". In the dilation, we expand the defect image, by adding beads adjacent to defective beads into the defect image. This is repeated cinvasions times. In the erosion, we contract the defect image, by removing beads adjacent to non-defective beads from the defect image. (Erosion of the defect image is equivalent to a dilation of the non-defective image.)
最后，我们“关闭”的形象，以填补缺陷图像中的小的差距。这包括了“扩张”和“侵蚀”。我们在扩张，扩大缺陷的形象，由缺陷的图像添加到相邻缺陷珠的珠。这是重复cinvasions倍。在侵蚀，我们承包的缺陷图像，通过消除缺陷图像相邻的珠子，无缺陷的珠子。 （缺陷图像的侵蚀是相当于一个无缺陷图像的扩张。）


值----------Value----------

A vector consisting of the BeadIDs of beads labelled as compact defects.
一个向量组成的紧凑缺陷标记的珠BeadIDs。


作者（S）----------Author(s)----------


Jonathan Cairns



参考文献----------References----------



参见----------See Also----------

BASH, generateNeighbours
BASH，generateNeighbours


举例----------Examples----------



## Not run: [＃无法运行：]

if(require(beadarrayExampleData)){

data(exampleBLData)
o <- BASHCompact(getBeadData(exampleBLData,array=1,what="Grn"), getBeadData(exampleBLData,array=1,what="ProbeIDs"))
o &lt;- BASHCompact(getBeadData(exampleBLData,array=1,what="Grn"), getBeadData(exampleBLData,array=1,what="ProbeIDs"), cinvasions = 10) ##increased no of closure invasions[＃增加没有封闭入侵]
o &lt;- BASHCompact(getBeadData(exampleBLData,array=1,what="Grn"), getBeadData(exampleBLData,array=1,what="ProbeIDs"), cutoff = 12) ##only larger defects will be found with this setting[＃只有较大的缺陷，会发现此设置]

}


## End(Not run)[＃结束（不运行）]

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


注：
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