fuzzy.ebam(siggenes)
fuzzy.ebam()所属R语言包：siggenes
EBAM and SAM for Fuzzy Genotype Calls
eBAM和SAM模糊基因型分型
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Computes the required statistics for an Empirical Bayes Analysis of Microarrays (EBAM; Efron et al., 2001) or a Significant Analysis of Microarrays (SAM; Tusher et al., 2001), respectively, based on the score statistic proposed by Louis et al. (2010) for fuzzy genotype calls or approximate Bayes Factors (Wakefield, 2007) determined using this score statistic.
计算所需的经验Bayes分析微阵列（EBAM。;埃弗龙等，2001）的统计显着性分析的基因芯片（山姆;等Tusher的，2001年），分别根据路易斯等人提出的得分统计， 。 （2010年）确定了模糊的的基因型分型或近似的贝叶斯因子（韦克菲尔德，2007年），使用这个得分统计。
Should not be called directly, but via ebam(..., method = fuzzy.ebam) or sam(..., method = fuzzy.stat), respectively.
不应直接，但通过ebam(..., method = fuzzy.ebam)或sam(..., method = fuzzy.stat)，分别被称为。
用法----------Usage----------
fuzzy.ebam(data, cl, type = c("asymptotic", "permutation", "abf"), W = NULL,
logbase = exp(1), addOne = TRUE, df.ratio = NULL, n.interval = NULL,
df.dens = 5, knots.mode = TRUE, type.nclass = c("FD", "wand", "scott"),
fast = FALSE, B = 100, B.more = 0.1, B.max = 30000, n.subset = 10, rand = NA)
fuzzy.stat(data, cl, type = c("asymptotic", "permutation", "abf"), W = NULL,
logbase = exp(1), addOne = TRUE, B = 100, B.more = 0.1, B.max = 30000,
n.subset = 10, rand = NA)
参数----------Arguments----------
参数：data
a matrix containing fuzzy genotype calls. Such a matrix can, e.g., be generated by the function getMatFuzzy based on the confidences for the three possible genotypes computed by preprocessing algorithms such as CRLMM.
矩阵模糊型分型。这样一个矩阵，例如，由函数生成的getMatFuzzy预处理算法由CRLMM如计算的三种可能的基因型机密的基础上。
参数：cl
a vector of zeros and ones specifying which of the columns of data contains the fuzzy genotype calls for the cases (1) and which the controls (0). Thus, the length of cl must be equal to the number of columns of data.
零和指定列的向量data包含的模糊的情况下，基因型分型（1）和对照组（0）。因此，长cldata列数必须是平等的。
参数：type
a character string specifying how the analysis should be performed. If "asymptotic", the trend statistic of Louis et al. (2010) is used directly, and EBAM or SAM are performed assuming that under the null hypothesis this test statistic follows am asymptotic standard normal distribution. If "permutation", a permutation procedure is employed to estimate the null distribution of this test statistic. If "abf", Approximate Bayes Factors (ABF) proposed by Wakefield (2007) are determined from the trend statistic, and EBAM or SAM are performed on these ABFs or transformations of these ABFs (see in particular logbase and addOne). In the latter case, again, a permutation procedure is used in EBAM and SAM to, e.g., compute posterior probabilities of association.
一个字符串，指定分析应如何进行。如果"asymptotic"，路易斯等人的趋势统计。 （2010）直接使用，和EBAM或SAM进行假设，零假设下检验统计如下上午渐近标准正态分布。如果"permutation"，置换过程估计这个检验统计量的零分布。如果"abf"，近似贝氏因子（ABF）的韦克菲尔德（2007年）提出确定从趋势统计，和EBAM或SAM在这些ABFS这些ABFS或转换（见特别logbase“ addOne）。再次，在后一种情况下，置换过程eBAM和SAM使用，例如，计算后验概率的关联。
参数：W
the prior variance. Must be either a positive value or a vector of length nrow(data) consisting of positive values. Ignored if type = "asymptotic" or type = "permutation". For details, see abf.
前变异。必须是一个积极的价值或长度nrow(data)正面的价值观组成的向量。如果type = "asymptotic"或type = "permutation"忽略。有关详细信息，请参阅abf。
参数：logbase
a numeric value larger than 1. If type = "abf", then the ABFs are not directly used in the analysis, but a log-transformation (with base logbase) of the ABFs. If the ABFs should not be transformed, logbase can be set to NA. Ignored if type = "asymptotic" or type = "permutation".
一个数字值大于1。 type = "abf"如果，然后ABFS不能直接用于分析，但改造的ABFSlog（碱基logbase）。如果ABFS不应转化，logbase可以设置为NA。如果type = "asymptotic"或type = "permutation"忽略。
参数：addOne
should 1 be added to the ABF before it is log-transformed? If TRUE, log(ABF + 1, base=logbase) is used as test score in EBAM or SAM. If FALSE, log(ABF, base = logbase) is considered. Only taken into account when type = "abf" and logbase is not NA.
1应该被添加到之前数转换的债券基金？如果TRUE，log(ABF + 1, base=logbase)被用来作为测试得分在EBAM或SAM。如果FALSE，log(ABF, base = logbase)被视为。只考虑type = "abf"和logbase不NA。
参数：df.ratio
integer specifying the degrees of freedom of the natural cubic spline used in the logistic regression with repeated observations for estimating the ratio f0/f. Ignored if type = "asymptotic". If not specified, df.ratio is set to 3 if type = "abf", and to 5 if type = "permutation"
整数，指定在反复观察logistic回归自然三次样条线估计比例f0/f的自由程度。如果type = "asymptotic"忽略。如果没有指定，df.ratio设置为3如果type = "abf"，5如果type = "permutation"
参数：n.interval
the number of intervals used in the logistic regression with repeated observations (if type = "permutation" or type = "abf"), or in the Poisson regression used to estimate the density of the observed z-values (if type = "asymptotic"). If NULL, n.interval is estimated by the method specified by type.nclass, where at least 139 intervals are considered if type = "permutation" or type = "abf".
logistic回归与重复观测使用的时间间隔的数量（如果如果type = "permutation"或type = "abf"），或在使用泊松回归估计观测到的z值的密度（ type = "asymptotic"）。如果NULL，如果n.interval或type.nclasstype = "permutation"type = "abf"，其中至少有139间隔被认为是由指定的方法估计。
参数：df.dens
integer specifying the degrees of freedom of the natural cubic spline used in the Poisson regression to estimate the density of the observed z-values in an application of ebam with type = "asymptotic". Otherwise, ignored.
整数，指定使用泊松回归估计观测到的z值在ebam与type = "asymptotic"应用的密度自然立方样条的自由程度。否则，忽略。
参数：knots.mode
logical specifying whether the df.dens - 1 knots are centered around the mode and not the median of the density when fitting the Poisson regression model to estimate the density of the observed z-values in an application of ebam with type = "asymptotic" (for details on this density estimation, see denspr). Ignored if type = "permutation" or type = "abf".
逻辑指定是否df.dens - 1节围绕“模式，而不是密度的中位数拟合泊松回归模型估计密度观测到的z值<申请时， X>用ebam（这个密度估计的详情，请参阅type = "asymptotic"）。如果denspr或type = "permutation"忽略。
参数：type.nclass
character string specifying the procedure used to compute the number of cells of the histogram. Ignored if type = "permutation", type = "abf", or n.interval is specified. Can be either "FD" (default), "wand", or "FD". For details, see denspr.
字符串指定的程序，用来计算直方图的单元数量。如果type = "permutation"，type = "abf"或n.interval指定忽略。可以是"FD"（默认），"wand"或"FD"。有关详细信息，请参阅denspr。
参数：fast
if FALSE the exact number of permuted test scores that are more extreme than a particular observed test score is computed for each of the variables/SNPs. If TRUE, a crude estimate of this number is used.
如果FALSE置换的测试成绩是超过一个特定的观察测试得分的极端的确切数目计算每个变量/单核苷酸多态性。如果TRUE，用于粗略估计这个数字。
参数：B
the number of permutations used in the estimation of the null distribution, and hence, in the computation of the expected z-values. Ignored if type = "asymptotic".
排列在空分布的估计使用人数，因此，在预期z值的计算。如果type = "asymptotic"忽略。
参数：B.more
a numeric value. If the number of all possible permutations is smaller than or equal to (1+B.more)*B, full permutation will be done. Otherwise, B permutations are used.
一个数值。如果所有可能的排列数小于或等于（1 +B.more）*B，全置换将完成。否则，使用B排列。
参数：B.max
a numeric value. If the number of all possible permutations is smaller than or equal to B.max, B randomly selected permutations will be used in the computation of the null distribution. Otherwise, B random draws of the group labels are used.
一个数值。如果所有可能的排列数小于或等于B.max的，B随机选择的排列将在空分布的计算。否则，B随机组标签提请使用。
参数：n.subset
a numeric value indicating in how many subsets the B permutations are divided when computing the permuted z-values. Please note that the meaning of n.subset differs between the SAM and the EBAM functions.
B排列分为许多子集时计算置换z值表示的数值。请注意，n.subset意义之间的SAM和EBAM的功能不同。
参数：rand
numeric value. If specified, i.e. not NA, the random number generator will be set into a reproducible state.
数值。如果指定，即不NA，随机数发生器将被设置成一个可重复的状态。
值----------Value----------
A list containing statistics required by ebam or sam.
列表包含ebam或sam需要的统计数据。
作者（S）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schw@gmx.de">holger.schw@gmx.de</a>
参考文献----------References----------
Empirical Bayes Analysis of a Microarray Experiment, JASA, 96, 1151-1160.
Association Tests that Accommodate Genotyping Errors. In Bernardo, J.M., Bayarri, M.J., Berger, J.O., Dawid, A.P., Heckerman, D., Smith, A.F.M., and West, M. (eds.), Bayesian Statistics 9, 393-420. Oxford University Press, Oxford, UK. With Discussion.
Applied to the Ionizing Radiation Response. PNAS, 98, 5116-5121.
Epidemiology Studies. AJHG, 81, 208-227.
参见----------See Also----------
ebam, sam, EBAM-class, SAM-class
ebam，sam，EBAM-class，SAM-class
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 2012-2-26 14:12:39
