CGHcall(CGHcall)
CGHcall()所属R语言包：CGHcall
Calling aberrations for array CGH tumor profiles.
调用阵列比较基因组杂交瘤型材的畸变。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Calls aberrations for array CGH data using a six state mixture model.
要求使用6个国家的混合模型的array CGH数据的畸变。
用法----------Usage----------
CGHcall(inputSegmented, prior = "auto", nclass = 4, organism = "human", robustsig="yes", nsegfit=3000, maxnumseg=100, minlsforfit=0.5)
参数----------Arguments----------
参数：inputSegmented
An object of class cghSeg
一个对象的类cghSeg
参数：prior
Options are all, not all, or auto. See details for more information.
选项是all，not all或auto。详情请参阅更多信息。
参数：nclass
The number of levels to be used for calling. Either 3 (loss, normal, gain) or 4 (including amplifications).
级别数将用于调用。要么3（损失，正常，增益）或4（包括扩增）。
参数：organism
Either human or other. This is only used for chromosome arm information when prior is set to all or auto (and samplesize > 20).
要么human或other。这仅仅是用于染色体臂的信息时prior设置为all或auto（和采样大小> 20）。
参数：robustsig
Options are yes or no. yes enforces a lower bound on the standard deviation of the normal segments
选项是yes或no。 yes执行正常段的标准偏差下限
参数：nsegfit
Maximum number of segments used for fitting the mixture model. Posterior probabilities are computed for all segments
装修混合模型使用的段的最大数量。后验概率计算各阶层
参数：maxnumseg
Maximum number of segments per profile used for fitting the model
每个配置文件的段的最大数量用于拟合模型
参数：minlsforfit
Minimum length of the segment (in Mb) to be used for fitting the model
段的最小长度（MB）可用于拟合模型
Details
详情----------Details----------
Please read the article and the supplementary information for detailed information on the algorithm. The parameter prior states how the data is used to determine the prior probabilities. When set to all, the probabilities are determined using the entire genome of each sample. When set to not all probabilites are determined per chromosome for each sample when organism is set to other or per chromosome arm when organism is human. The chromosome arm information is taken from the March 2006 version of the UCSC database. When prior is set to auto, the way probabilities are determined depends on the sample size. The entire genome is used when the sample size is smaller than 20, otherwise chromosome (arm) information is used. Please note that CGHcall uses information from all input data to determine the aberration probabilities. When for example triploid or tetraploid tumors are observed, we advise to run CGHcall separately on those (groups of) samples. Note that robustsig = yes enforces the sd corresponding to the normal segments to be at least half times the pooled gain/loss sd. Use of "nsegfit" significantly lower computing time with respect to previous CGHcall versions without much accuracy loss. Moreover, "maxnumseg" decreases the impact on the results of profiles with inferior segmentation results. Finally, "minlsforfit" decreases the impact of very small aberations (potentially CNVs rather than CNAs) on the fit of the model. Note that always a result for all segments is produced. IN MOST CASES, CGHcall SHOULD BE FOLLOWED BY FUNCTION ExpandCGHcall.
请仔细阅读文章的补充资料，对算法的详细信息。参数prior规定使用的数据是如何确定先验概率。当设置为all，概率确定每个样本的整个基因组。当设置为not allprobabilites每染色体确定每个样品时organism设置为other％或染色体臂当organism是human。染色体臂的信息是从2006年3月的UCSC数据库的版本。当prior设置为auto的概率确定方法，样本大小取决于。使用时，样本大小是小于20，否则染色体（臂）的信息用于整个基因组。请注意，CGHcall使用所有输入数据信息，以确定畸变的概率。例如，当三倍体或四倍体肿瘤的观察，我们建议上运行（组）样品CGHcall分开。注意robustsig =yes强制执行的SD相应的正常段，至少有一半时间是汇集的收益/亏损SD的。使用“nsegfit”显着降低计算时间方面没有太多的精度损失的的以前CGHcall版本。此外，“maxnumseg”减少对型材的结果较差的分割结果的影响。最后，“minlsforfit”减少（而不是潜在的CNVs的CNA）的模型拟合很小aberations的影响。请注意，始终是各阶层的结果产生。在大多数情况下，CGHcall应遵循功能ExpandCGHcall。
值----------Value----------
This function return a list with five components:
这个函数返回列表五部分组成：
参数：posteriorfin2
Matrix containing call probabilities for each segment. First column denotes profile number, followed by k columns with aberration probabilities for each sample, where k is the number of levels used for calling (nclass).
矩阵包含每个段的呼叫的概率。第一列表示的文件数量，k列与畸变的概率对每个样品，其中k是用于调用（nclass）的水平。
参数：nclone
Number of clone or probes
克隆或探针数
参数：nc
Number of samples
样本数
参数：
Number of classes used
使用的类的数量
参数：regionsprof
Matrix containing information about the segments, 4 colums: profile, start probe, end probe, segmented value
有关分部，4 colums：个人主页上，启动探针，年底探针，分段值矩阵包含的信息
作者（S）----------Author(s)----------
Sjoerd Vosse & Mark van de Wiel
参考文献----------References----------
参见----------See Also----------
ExpandCGHcall
ExpandCGHcall
举例----------Examples----------
data(Wilting)
## Convert to cghRaw object[＃转换为对象cghRaw]
cgh <- make_cghRaw(Wilting)
print(cgh)
## First preprocess the data[＃首先进行预处理数据]
raw.data <- preprocess(cgh)
## Simple global median normalization for samples with 75% tumor cells[＃简单的全球75％的肿瘤单元样本中位数标准化]
perc.tumor <- rep(0.75, 3)
normalized.data <- normalize(raw.data, cellularity=perc.tumor)
## Segmentation with slightly relaxed significance level to accept change-points.[＃分割稍微宽松的显着性水平，接受变化点。]
## Note that segmentation can take a long time.[＃注意，分割可以采取很长一段时间。]
## Not run: segmented.data <- segmentData(normalized.data, alpha=0.02)[＃无法运行：segmented.data < - segmentData（normalized.data，α= 0.02）]
## Not run: postsegnormalized.data <- postsegnormalize(segmented.data)[＃无法运行：postsegnormalized.data < - postsegnormalize（segmented.data）]
## Call aberrations[＃呼叫畸变的]
## Not run: result <- CGHcall(postsegnormalized.data)[＃无法运行结果< - CGHcall（postsegnormalized.data）]
## Expand to CGHcall object[＃展开CGHcall对象的]
## Not run: result <- ExpandCGHcall(result,postsegnormalized.data)[＃无法运行结果< - ExpandCGHcall（结果，postsegnormalized.data）]
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 2012-2-25 14:35:17
