generateNeighbours(beadarray)
generateNeighbours()所属R语言包：beadarray
Generate matrix of neighbouring beads
生成矩阵邻近珠
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Generates a neighbours matrix from either a .locs file or the X and Y coordinates in a beadLevelData object.
一个邻居矩阵生成一个。LOCS文件或X和Y坐标beadLevelData对象。
用法----------Usage----------
generateNeighbours(BLData, array = 1, useLocs = TRUE, window = 30, margin = 10, thresh = 2.2)
参数----------Arguments----------
参数：BLData
An object of class beadLevelData-class
一个对象的类beadLevelData-class
参数：array
integer specifying which section/array to process
整数，指定处理该条/阵列
参数：useLocs
logical value, specifiying whether the .locs file (if present) should be used to determine neighbours.
逻辑值，specifiying。LOCS文件（如果存在）是否应该被用来确定邻居。
参数：window
numeric value, specifying window size (see below)
数值，指定窗口大小（见下文）
参数：margin
numeric value, specifying size of window margin (see below)
数值，指定窗口大小保证金（见下文）
参数：thresh
numeric value, which determines how large links are removed. (see below)
数值，这就决定了多大的链接都被删除。 （见下文）
Details
详情----------Details----------
generateNeighbours determines, for each bead on the array, which beads are next to it. It assumes that the beads are in a hexagonal lattice.
generateNeighbours决定，为每个阵列上，旁边的珠珠。它假定，在一个六角形晶格珠。
If the .locs file is present and useLocs = TRUE then the ordering of the .locs file is used to infere the grid layout. This is far quicker than the alternative and is thus recommended, but can only be used on BeadChip platforms. If the data is from a Sentrix Array useLocs is automatically set to FALSE and the following algorithm is applied instead.
如果.locs文件是当前和useLocs = TRUE然后订购.locs文件用于infere网格布局。这是远远快于替代品，因此建议，但只能使用BeadChip平台。如果数据从Sentrix阵列useLocs的是被自动设置为FALSE和应用，而不是下面的算法。
The algorithm used first links each bead to its 6 closest neighbours. It then removes the longest link if its squared length is more than thresh multiplied by the squared length of the next longest link. A similar process is applied to the 2nd and 3rd longest links.
所使用的算法每个环节珠其最近的邻居。然后删除最长的环节，如果它的平方长度比thresh下最长链接平方长度乘以。一个类似的过程适用于第二和第三个最长链接。
Finally, any one way links are removed (i.e. a link between two beads is only preserved if each bead considers the other to be its neighbour).
最后，任何一种方式联系被删除（即只保留两个珠子之间的联系，如果每个珠认为是它的邻居）。
To ease computation, the algorithm only computes neighbours of beads in a square window of side length 2*(window) which travels across the array. Beads in a margin around the square, of width (margin), are also considered as possible neighbours.
为了简化计算，该算法只计算在一个边长的正方形窗口2*(window)横跨阵列旅行珠的邻居。在广场周围的保证金，宽度，珠(margin)，也考虑尽可能的邻居。
值----------Value----------
A matrix with 6 columns. Each row corresponds to a bead in the passed beadLevelData-class and the six entries are the indices of the 6 neighbouring beads. Values of NA indicate that the neighbouring bead appears to be missing, either due to failing Illumina's decoding or being at the edge of the array.
与6列的矩阵。每一行对应到珠在传递beadLevelData-class和6项指数的6个邻国珠。的NA值表示，邻近珠似乎缺少，由于未能Illumina的解码或阵列的边缘。
作者（S）----------Author(s)----------
Jonathan Cairns, Mike Smith
参考文献----------References----------
beadarray, BASH and HULK - tools to increase the value of Illumina BeadArray experiments. In A. Gusnato, K.V. Mardia, & C.J. Fallaize (eds), Statistical Tools for Challenges in Bioinformatics. 2009 pp. 33-37. Leeds, Leeds University Press.
参见----------See Also----------
HULK, BASH
HULK，BASH
举例----------Examples----------
## Not run: [＃无法运行：]
if(require(beadarrayExampleData)){
data(exampleBLData);
neighbours <- generateNeighbours(exampleBLData, array = 1, useLocs = FALSE);
}
## 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：
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 12:41:26
