colTDTsam(trio)
colTDTsam()所属R语言包：trio
SAM and EBAM for Trio Data
为SAM和EBAM的三重奏数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs a Significance Analysis of Microarrays (SAM; Tusher et al., 2001) or an Empirical Bayes Analysis of Microarrays (EBAM; Efron et al., 2001), respectively, based on the genotypic transmission/disequilibrium test statistic.
进行显着性分析的基因芯片“（SAM Tusher等，2001）或经验Bayes分析微阵列（EBAM埃弗龙等人，2001），分别传递/不平衡检验统计量的基因型的基础上。
用法----------Usage----------
colTDTsam(mat.snp, model = c("additive", "dominant", "recessive", "max"),
approx = NULL, B = 1000, size = 10, chunk = 100, rand = NA)
colTDTebam(mat.snp, model = c("additive", "dominant", "recessive", "max"),
approx = NULL, B = 1000, size = 10, chunk = 100,
n.interval = NULL, df.ratio = 3, df.dens = 3, knots.mode = TRUE,
type.nclass = c("wand", "FD", "scott"), fast = FALSE, rand = NA)
参数----------Arguments----------
参数：mat.snp
a matrix in genotype format, i.e. a numeric matrix in which each column is a vector of length 3 * t representing a SNP genotyped at t trios. Each of the t blocks of rows in mat.snp must consist of the genotypes of father, mother, and offspring (in this order), where the genotypes must be coded by 0, 1, and 2. Missing values are allowed and need to be coded by NA. This matrix might be generated from a data frame in ped format by, e.g., employing ped2geno.
基因型格式矩阵，即数字矩阵中的每一列是一个向量的长度3 * t代表一个SNP基因分型t三重奏。每个t块中的行mat.snp必须由的基因型的父亲，母亲和后代（按照这个顺序），基因型必须被编码为0，1和2。遗漏值是允许的，需要进行编码NA。这个矩阵可能产生的PED格式的数据框中，例如，采用ped2geno。
参数：model
type of genetic mode of inheritance that should be considered. Either "additive" (default), "dominant", "recessive", or "max". If model = "max", the maximum over the gTDT statistics for testing an additive, dominant, and recessive model is used as gTDT statistic. Abbreviations are allowed. Thus, e.g., model = "dom" will fit a dominant model, and model = "r" an recessive model.
应被视为遗传继承模式类型。无论是"additive"（默认），"dominant"，"recessive"或"max"。如果model = "max"，最大以上的gTDT的统计测试添加剂，显性和隐性模型被用来作为gTDT统计。缩写是允许的。因此，例如，model = "dom"会适合一个占主导地位的模式，和model = "r"隐性模型。
参数：approx
logical specifying whether the null distribution should be approximated by a ChiSquare-distribution with one degree of frredom. If approx = FALSE, the null distribution is estimated based on a permutation method. If not specified, i.e. NULL, approx is set to TRUE, when an additive, dominant, or recessive mode of inheritance is considered, and approx = FALSE, when model = "max". If model = "max", it is not allowed to set approx = TRUE.
逻辑指定是否为null分布应近似于一个ChiSquare分配有一个度的frredom。如果approx = FALSE，空分布的估计基础上的一个置换方法。如果未指定，例如NULL，approx设置为TRUE，被认为是一种添加剂，显性或隐性的遗传方式时，和approx = FALSE，当<X >。 model = "max"如果，它是不允许，设置model = "max"。
参数：B
number of permutations used in the estimation of the null distribution, and thus, the computation of the null statistics. Ignored if approx = TRUE.
零分布的估计中使用的排列数目，并且因此，计算空统计数字。如果忽略approx = TRUE。
参数：size
number of SNPs considered simultaneously when computing the gTDT statistics.
考虑的SNP位点的数量，同时计算gTDT统计。
参数：chunk
number of permutations considered simultaneously in the permutation procedure.
在置换过程中同时考虑的排列数目。
参数：n.interval
the number of intervals used in the logistic regression with repeated observations for estimating the ratio of the null density to the density of the observed gTDT values in an EBAM analysis (if approx = FALSE), or in the Poisson regression used to estimate the density of the observed gTDT values (if approx = TRUE). For details, see Efron et al., 2001, or Schwender and Ickstadt, 2008, respectively. If NULL, n.interval is determined by the maximum of 139 (see Efron et al., 2001) and the number of intervals estimated by the method specified by type.nclass.
的数量与重复观察中使用的Logistic回归估计空密度的比率到的密度在EBAM分析的的观测gTDT值（如果approx = FALSE），或在使用的泊松回归估计的时间间隔的密度的观察到的gTDT值（：如果approx = TRUE）。有关详细信息，请参阅埃弗龙等人，2001年，或Schwender和Ickstadt，2008年分别。如果NULL，n.interval是由最大的139（见埃弗龙等人，2001年）和区间估计的方法指定的type.nclass。
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 of the null density to the density of the observed gTDT values in an EBAM analysis. Only used when approx is set to FALSE.
整数，指定反复观察估计空密度的比率在EBAM分析的的观测gTDT值密度的Logistic回归自然三次样条中使用的程度的自由。仅用于approx设置为FALSE。
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 gTDT values in an EBAM analysis. Only used when approx is set to TRUE.
整数，指定使用泊松回归估计在EBAM分析的的观测gTDT值的密度的自然三次样条的自由程度。仅用于approx设置为TRUE。
参数：knots.mode
logical specifying whether the df.dens - 1 knots of the natural cubic spline 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 gTDT values in an EBAM analysis. Only used when approx is set to TRUE. For details on this density estimation, see denspr.
逻辑指定是否df.dens - 1海里的自然三次样条为中心的模式，而不是装修时的密度中位数的泊松回归模型估计的的观察到gTDT的值在一个EBAM的分析的密度。仅用于approx设置为TRUE。这个密度估计的详细信息，请参阅denspr。
参数：type.nclass
character string specifying the procedure used to estimate the number of intervals of the histogram used in the logistic regression with repeated observations or the Poisson regression, respectively (see n.interval). Can be either "wand" (default), "FD", or "scott". Ignored if n.interval is specified. For details, see denspr.
字符的字符串指定程序用于估计数间隔的直方图反复观察或泊松回归，logistic回归（见n.interval的）。可以是"wand"（默认），"FD"或"scott"。如果忽略n.interval指定。有关详细信息，请参阅denspr。
参数：fast
logical specifying whether a crude estimate for the number of permuted test scores larger than the respective observed gTDT value should be used. If FALSE, the exact number of permuted test scores larger than the respective observed gTDT value is computed.
逻辑指定是否置换考试成绩大于各自观察到的gTDT值的数量，应使用一个粗略的估计。如果FALSE，置换考试成绩大于各自观察到的gTDT值的确切数字计算。
参数：rand
numeric value. If specified, i.e. not NA, the random number generator will be set into a reproducible state.
数值。如果指定的话，即不NA，随机数生成器将被设置成一个可重复的状态。
值----------Value----------
The output of colTDTsam or colTDTebam is an object of class SAM or EBAM, respectively. All the features implemented in the R package siggenes for an SAM or EBAM analysis, respectively, can therefore be used in the SAM or EBAM analysis of case-parent trio data implemented in colTDTsam or colTDTebam, respectively. For details, see sam or ebam, respectively.
的输出colTDTsam或colTDTebam是一个对象类SAM或EBAM，分别。在R包实现的功能siggenes为SAM或EBAM分析，分别，因此可以使用在SAM或EBAM的分析，情况下母公司三人数据在colTDTsam或实施colTDTebam“。有关详细信息，请参阅sam或ebam，分别。
（作者）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schwender@udo.edu">holger.schwender@udo.edu</a>
参考文献----------References----------
Empirical Bayes Analysis of a Microarray Experiment, Journal of the American Statistical Association, 96, 1151-1160.
BMC Bioinformatics, 9, 144.
Rapid Testing of SNPs and Gene-Environment Interactions in Case-Parent Trio Data Based on Exact Analytic Parameter Estimation. Biometrics. DOI: 10.1111/j.1541-0420.2011.01713.x.
Applied to the Ionizing Radiation Response. Proceedings of the National Academy of Science of the United States of America, 98, 5116-5121.
参见----------See Also----------
colTDT, colTDTmaxStat, sam, ebam, SAM-class, EBAM-class
colTDT，colTDTmaxStat，sam，ebam，SAM-class，EBAM-class
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-10-1 12:05:28
