find.genomic.events(aCGH)
find.genomic.events()所属R语言包：aCGH
Finds the genomic events associated with each of the array CGH samples
发现每个阵列比较基因组杂交样品的基因组事件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Finds the genomic events associated with each of the array CGH samples. Events include whole chromosomal gains and losses, aberrations, transitions, amplifications and their respective counts and sizes. The hmm states has to be computed before using this function.
发现每个阵列比较基因组杂交样品的基因组事件。活动包括整个染色体的收益和损失，畸变，过渡，扩增和各自的数量和规模。 HMM的状态，必须使用此功能之前计算。
用法----------Usage----------
find.genomic.events(aCGH.obj, maxChrom = 23, factor = 5, maxClones = 1,
maxLen = 1000, absValSingle = 1, absValRegion = 1,
diffVal1 = 1, diffVal2 = .5, maxSize = 10000,
pChrom.min = .9, medChrom.min = .1)
参数----------Arguments----------
参数：aCGH.obj
Object of class aCGH.
对象类aCGH。
参数：maxChrom
Highest chromosomal number to find events.
最高的染色体数目找到事件。
参数：factor
Determines outliers. See findOutliers.func.
确定离群。看到findOutliers.func。
参数：maxClones
Determines aberrations. See findAber.func.
决定畸变。看到findAber.func。
参数：maxLen
Determines aberrations. See findAber.func.
决定畸变。看到findAber.func。
参数：absValSingle
Determines amplifications. See findAmplif.func.
决定扩增。看到findAmplif.func。
参数：absValRegion
Determines amplifications. See findAmplif.func.
决定扩增。看到findAmplif.func。
参数：diffVal1
Determines amplifications. See findAmplif.func.
决定扩增。看到findAmplif.func。
参数：diffVal2
Determines amplifications. See findAmplif.func.
决定扩增。看到findAmplif.func。
参数：maxSize
Determines amplifications. See findAmplif.func.
决定扩增。看到findAmplif.func。
参数：pChrom.min
Determines whole chromosomal gains and losses. Chromosome should contain no transitions, have its absolute median equal or greater than medChrom.min and at least medChrom.min has to be greater or less than 0.
确定整个染色体的收益和损失。染色体应该包含没有变，有其绝对的中位数大于或等于medChrom.min和至少medChrom.min有大于或小于0。
参数：medChrom.min
Determines whole chromosomal gains and losses. Chromosome should contain no transitions, have its absolute median equal or greater than medChrom.min and at least medChrom.min has to be greater or less than 0.
确定整个染色体的收益和损失。染色体应该包含没有变，有其绝对的中位数大于或等于medChrom.min和至少medChrom.min有大于或小于0。
Details
详情----------Details----------
The default parameters generally work. Threshold for merging may be changed depending on the expected normal cell contamination and/or expected magnitude of the changes. AIC model generally works, however, may need to be readjusted depending on how liberal or conservative one wants to be in finding genomic events. We recommend BIC criterion with delta = 1 for noisier data.
默认参数一般工作。合并的阈值可能会改变，取决于预期的正常单元污染和/或预期的变化幅度。 AIC的模型一般工作，然而，可能需要调整取决于自由派或者保守派的人想的是在寻找基因组事件。我们建议的BICDelta= 1的标准，噪音数据。
值----------Value----------
参数：num.transitions
matrix of dimensions maxChrom by number of samples. It contains number of transitions that were recorded on a given chromosome for a given sample.
尺寸maxChrom矩阵的样本数量。它包含了被记录在一个给定的样本染色体的过渡。
参数：num.amplifications
matrix of dimensions maxChrom by number of samples It contains number of amplifications that were recorded on a given chromosome for a given sample.
尺寸maxChrom样本数的矩阵，它包含了被记录在一个给定的样本染色体的扩增数量。
参数：num.aberrations
matrix of dimensions maxChrom by number of samples. It contains number of focal aberrations that were recorded on a given chromosome for a given sample.
尺寸maxChrom矩阵的样本数量。它包含的焦距被记录在一个给定的样本染色体畸变。
参数：num.outliers
matrix of dimensions maxChrom by number of samples. It contains number of outliers that were recorded on a given chromosome for a given sample.
尺寸maxChrom矩阵的样本数量。它包含了被记录在一个给定的样本染色体的离群数。
参数：num.transitions.binary
binary matrix of dimensions maxChrom by number of samples. Non-zero entry indicates whether 1 or more transitions were recorded on a given chromosome for a given sample.
尺寸maxChrom样本数的二进制矩阵。非零项指示是否对于一个给定的样本染色体上记录1个或更多的过渡。
参数：num.amplifications.binary
binary matrix of dimensions maxChrom by number of samples. Non-zero entry indicates whether 1 or more amplifications were recorded on a given chromosome for a given sample.
尺寸maxChrom样本数的二进制矩阵。非零项指示是否对于一个给定的样本染色体上记录1个或更多的扩增。
参数：num.aberrations.binary
binary matrix of dimensions maxChrom by number of samples. Non-zero entry indicates whether 1 or more focal aberrations were recorded on a given chromosome for a given sample.
尺寸maxChrom样本数的二进制矩阵。非零项指示是否记录对于一个给定的样本染色体上的1个或多个联络像差。
参数：num.outliers.binary
binary matrix of dimensions maxChrom by number of samples. Non-zero entry indicates whether 1 or more outliers were recorded on a given chromosome for a given sample.
尺寸maxChrom样本数的二进制矩阵。非零项指示是否对于一个给定的样本染色体上1个或多个离群记录。
参数：whole.chrom.gain.loss
matrix of dimensions maxChrom by number of samples. Positive entry indicates that a given chromosome was gained in a given sample, negative entry indicates that a given chromosome was lost in a given sample, 0 entry is normal chromosome and NA marks chromosomes with one or more transition.
尺寸maxChrom矩阵的样本数量。正项表示，在一个给定的样本中获得一个给定的染色体，负条目表示一个特定的染色体，在一个给定的样本丢失，0项是正常的染色体和无标记染色体与一个或多个过渡。
参数：size.amplicons
matrix of dimensions maxChrom by number of samples. Reports size of a given chromosome that is amplified (kb units) in a given sample.
尺寸maxChrom矩阵的样本数量。报告一个给定的染色体，在一个给定的样本扩增（KB为单位）的大小。
参数：num.amplicons
matrix of dimensions maxChrom by number of samples. Reports number of disjoint amplicons on a given chromosome for a given sample.
尺寸maxChrom矩阵的样本数量。报告的数量定为一个给定的样本染色体上的不相交的扩增。
参数：outliers
list containing 3 matrices of dimensions number of clones by number of samples. See findOutliers.func.
列表中包含的样本数3尺寸克隆数的矩阵。看到findOutliers.func。
参数：aberrations
list containing a matrix of dimensions number of clones by number of samples. See findAber.func.
列出包含的样本数矩阵尺寸克隆。看到findAber.func。
参数：transitions
list containing 2 matrices of dimensions number of clones by number of samples. See findTrans.func.
列表，其中包含2尺寸克隆数矩阵的样本数量。看到findTrans.func。
参数：amplifications
list containing a matrix of dimensions number of clones by number of samples. See findAmplif.func.
列出包含的样本数矩阵尺寸克隆。看到findAmplif.func。
参见----------See Also----------
aCGH find.hmm.states mergeFunc findAber.func findTrans.func findAmplif.func findOutliers.func
aCGHfind.hmm.statesmergeFuncfindAber.funcfindTrans.funcfindAmplif.funcfindOutliers.func
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 2012-2-25 10:59:12
