runGLAD(snapCGH)
runGLAD()所属R语言包：snapCGH
Results of segmenting an aCGHList data object using the GLAD library
一个aCGHList数据对象使用高兴库分割结果
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function allows the detection of breakpoints in genomic profiles obtained by array CGH technology and affects a status (gain, normal or lost) to each clone. It requires that the library GLAD is loaded.
此功能允许阵列比较基因组杂交技术获得的基因组剖面的断点检测状态（增益，正常或丢失），并影响到每个克隆。它需要库GLAD加载。
用法----------Usage----------
runGLAD(input, smoothfunc="lawsglad", base=FALSE, sigma = NULL, bandwidth=10,
round=2, lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,
type="tricubic", param=c(d=6), alpha=0.001, method="centroid",
nmax=8, verbose=FALSE, ...)
参数----------Arguments----------
参数：input
An object of class MAList or SegList
一个对象类MAList或SegList
参数：smoothfunc
Type of algorithm used to smooth LogRatio by a piecewise constant function. Choose either lawsglad, aws::aws or aws::laws.
算法类型用于平滑分段常数函数LogRatio的。选择其中lawsglad，aws::aws或aws::laws。
参数：base
If TRUE, the position of clone is the physical position onto the chromosome, otherwise the rank position is used.
如果TRUE，克隆的位置是在染色体上的物理位置，否则的排名位置。
参数：sigma
Value to be passed to either argument sigma2 of aws::aws function or shape of aws::laws. If NULL, sigma is calculated from the data.
值被传递到任何一个参数sigma2aws::aws函数shapeaws::laws。如果NULL，Sigma是从数据计算。
参数：bandwidth
Set the maximal bandwidth hmax in the aws::aws or aws::laws function. For example, if bandwidth=10 then the hmax value is set to 10*X_N where X_N is the position of the last clone.
设置最大带宽hmaxaws::aws或aws::laws函数。例如，如果bandwidth=10hmax值设置为10 *X_N其中X_N最后克隆的立场。
参数：round
The smoothing results are rounded or not depending on the round argument. The round value is passed to the argument digits of the round function.
平滑结果四舍五入或不取决于round参数。 round值传递参数digits的round功能。
参数：lambdabreak
Penalty term (λ') used during the Optimization of the number of breakpoints step.
惩罚项（λ'）用于在断点一步优化。
参数：lambdacluster
Penalty term (λ*) used during the MSHR clustering by chromosome step.
惩罚项（λ*）期间，染色体步MSHR的聚类。
参数：lambdaclusterGen
Penalty term (λ*) used during the HCSR clustering throughout the genome step.
惩罚项（λ*）用于在整个基因组步HCSR聚类。
参数：type
Type of kernel function used in the penalty term during the Optimization of the number of breakpoints step, the MSHR clustering by chromosome step and the HCSR clustering throughout the genome step.
在点球术语使用过程中断点一步，通过染色体步的MSHR聚类和整个基因组步HCSR聚类优化的内核函数的类型。
参数：param
Parameter of kernel used in the penalty term.
在点球术语使用的内核的参数。
参数：alpha
Risk alpha used for the Outlier detection step.
风险阿尔法用于离群检测步骤。
参数：method
The agglomeration method to be used during the MSHR clustering by chromosome and the HCSR clustering throughout the genome clustering steps.
集聚在MSHR聚类染色体和整个基因组聚类步骤HCSR聚类方法。
参数：nmax
Maximum number of clusters (N*max) allowed during the the MSHR clustering by chromosome and the HCSR clustering throughout the genome clustering steps.
期间由染色体的MSHR的聚类和整个基因组聚类步骤HCSR聚类允许的最大簇数目（不适用*最大）。
参数：verbose
If TRUE some information are printed
如果TRUE一些信息打印
参数：...
...
...
Details
详情----------Details----------
For a detailed explanation of the GLAD algorithm please see the relevant section of the GLAD manual: glad
为高兴算法的详细说明，请参阅高兴手册的相关章节：glad
值----------Value----------
The function returns an object of class SegList
该函数返回一个对象类SegList
参见----------See Also----------
glad MAList runHomHMM runDNAcopy SegList
gladMAListrunHomHMMrunDNAcopySegList
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。
|
发表于 2012-2-26 14:35:45
