cutoff(MLDA)
cutoff()所属R语言包：MLDA
Determination of log likelihood ratio cut-offs for methylation and unmethylation
测定的甲基化和非甲基化对数似然比切销
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A function to determine the log likelihood ratio cut-offs for methylation and unmethylation in each sample
一个函数来确定每个样本中的甲基化和非甲基化对数似然比切销
用法----------Usage----------
cutoff(dataset, mlda.obj, IR = 0.01, CR = 1.4, ncut = 30,
unmeth.start = 1, meth.start = 1)
参数----------Arguments----------
参数：dataset
A dataset object from mlda.data()
一个DataSet对象从mlda.data（）
参数：mlda.obj
An object from mlda()
从MLDA的对象（）
参数：IR
Inconsistent rate for dye-swapped/duplicated arrays. Default is 0.01.
不一致的阵列为dye-swapped/duplicated率。默认值是0.01。
参数：CR
Consistent rate for dye-swapped/duplicated arrays. Default is 1.4.
一致阵列为dye-swapped/duplicated率。默认值是1.4。
参数：ncut
The number of threshold intervals of log likelihood ratio for unmethylation and methylation
非甲基化和甲基化的对数似然比的阈值的时间间隔的数目
参数：unmeth.start
The start value of threshold of log likelihood ratio for unmethylation
阈值的对数似然比的非甲基化的开始值
参数：meth.start
The start value of threshold of log likelihood ratio for methylation
阈值的对数似然比的甲基化的开始值
Details
详细信息----------Details----------
Two inconsistency rates(IRmeth and IRunmeth) and two consistency rates(CRmeth and CRunmeth) between dye-swapped/duplicated arrays were used to determine the log likelihood ratio cut-offs. IRmeth represents the rate of the microarray features identified as methylated in one array but as unmethylated in the other one, while IRunmeth is the rate of the microarray features identified as unmethylated in one array but as methylated in the other one. CRmeth and CRunmeth are the rates for the spots identified as methylated and unmethylated in both dye-swapped/duplicate arrays.
两个不一致的速率（IRmeth和IRunmeth）和两个的一致性的速率（CRmeth和CRunmeth）dye-swapped/duplicated阵列之间被用来确定对数似然比切口取舍。 IRmeth代表的微阵列的速率设有识别标识为甲基化在一个阵列中，但作为非甲基化中的另一个，而IRunmeth率的微阵列设有在一个阵列中，但是，未甲基化的甲基化中的另一个。 CRmeth和CRunmeth点甲基化和非甲基化在这两个dye-swapped/duplicate阵列的税率。
The log likelihood ratio thresholds for methylated and unmethyalted features, which kept the IR low (0.01) and CR high (1.4) were used as the cut-offs for the methylated and unmethylated loci. Empirically, IR tends to rise with the increase of CR slowly, but starts to increase dramatically when the CR goes above 1.4, at which point the inconsistency rate is generally about 0.01. Therefore, we use IR=0.01 and CR=1.4 by default.
甲基化和unmethyalted功能，从而保持IR低（0.01）和CR的高（1.4）的对数似然比的阈值被用作切割的甲基化和非甲基化的位点的平衡。根据经验，红外CR的增加慢慢上升的倾向，但开始急剧增加，当CR变为1.4以上，在该点的不一致率通常是约0.01。因此，我们使用默认情况下，IR = 0.01，CR = 1.4。
值----------Value----------
a list containing <table summary="R valueblock"> <tr valign="top"><td>lr.thres </td> <td> A matrix including cut-offs for unmethylation and methylation for each sample</td></tr> <tr valign="top"><td>rate </td> <td> A list of IRs and CRs calculated at various thresholds</td></tr> </table>
一个列表，其中包含<table summary="R valueblock"> <tr valign="top"> <TD> lr.thres </ TD> <td>一个矩阵，包括边界品位为每个样本的非甲基化和甲基化</ TD> </ TR> <tr valign="top"> <TD> rate </ TD> <td>一个列表国税局和CRS计算在不同的阈值</ TD> </ TR> </表>
（作者）----------Author(s)----------
Wei Dai <a href="mailto:w.dai@imperial.ac.uk">w.dai@imperial.ac.uk</a>
参见----------See Also----------
MLDA Examples are included
MLDA例子
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-9-23 12:29:50
