haplo.long(SimHap)
haplo.long()所属R语言包：SimHap
Haplotype analysis for longitudinal data
纵向数据的单倍型分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
haplo.long performes a series of linear mixed effects models using a simulation-based approach to account for uncertainty in haplotype assignment when phase is unknown.
haplo.long performes一系列线性混合效应模型，使用模拟为基础的方法来解释阶段是未知的单倍型分配的不确定性时。
用法----------Usage----------
haplo.long(fixed, random, pheno, haplo, cor=NULL,
value = 0.2, form=~1, sim, effect = "add", sub = NULL, adjust=FALSE)
参数----------Arguments----------
参数：fixed
as per lme. A two-sided linear formula object describing the fixed-effects part of the model including SNP parameters, with the response on the left of a ~ operator and the terms, separated by + operators.
如每lme。一个双面的线性公式对象描述固定效应的模型，包括SNP参数，左边的一个~运营商和条款上的响应，分离+运营商。
参数：random
as per lme. A one-sided formula of the form ~x1+...+xn | g1/.../gm, with x1+...+xn specifying the model for the random effects and g1/.../gm the grouping structure (m may be equal to 1, in which case no / is required). The random effects formula will be repeated for all levels of grouping, in the case of multiple levels of grouping.
如每lme。是一种片面的公式的形式~x1+...+xn | g1/.../gm与x1+...+xn指定型号的随机效应和g1/.../gm的分组结构（m可能是等于1，情况下，不/是必需的）。各级分组，多级分组的情况下，将重复的随机效应公式。
参数：pheno
a dataframe containing phenotype data.
一个数据框的表型数据。
参数：haplo
a haplotype object made by make.haplo.rare. The subjects must in the same order as they are in the phenotype data.
单倍型对象由make.haplo.rare。科目必须以相同的顺序，因为它们是在表型数据。
参数：cor
a corStruct object describing the within-group correlation structure. Available correlation structures are corAR1, corCAR1, and corCompSymm. See the documentation of corClasses for a description of these. Defaults to NULL corresponding to no within-subject correlation.
corStruct对象描述的组内相关结构。可供相关结构corAR1，corCAR1和corCompSymm等。查看的文档corClasses说明这些。默认值NULL对应于无内相关。
参数：value
for corAR1 - the value of the lag 1 autocorrelation, which must be between -1 and 1. For corCAR1 - the correlation between two observations one unit of time apart. Must be between 0 and 1. For corCompSymm - the correlation between any two correlated observations. Defaults to 0.2.
为corAR1 - 滞后1期自相关，它必须是-1到1之间的值。对于corCAR1 - 两个观测时间相隔的一个单元的之间的相关性。必须是在0和1之间。对于corCompSymm - 任何两个相关的观测之间的相关性。默认为0.2的。
参数：form
a one sided formula of the form ~ t, or ~ t | g, specifying a time covariate t and, optionally, a grouping factor g. A covariate for this correlation structure must be integer valued. When a grouping factor is present in form, the correlation structure is assumed to apply only to observations within the same grouping level; observations with different grouping levels are assumed to be uncorrelated. Defaults to ~ 1, which corresponds to using the order of the observations in the data as a covariate, and no groups.
一个双面式的形式~ t，或~ t | g，指定时间协变量t和，任选地，分组因子g。这种相关性结构的协变量必须是整数值。当一个分组因子是本form，相关结构被假定只适用于在同一分组级别的观测观测具有不同的分组水平被假定为是不相关的。默认~ 1，对应的使用顺序的意见作为协变量的数据，并没有组。
参数：sim
the number of simulations from which to evaluate the results.
的数量的模拟来对结果进行评估。
参数：effect
the haplotypic effect type: "add" for additive, "dom" for dominant and "rec" for recessive. Defaults to additive. See note.
单倍型的效果类型："add"添加剂"dom"主导和"rec"为隐性。默认至添加剂。见注。
参数：sub
optional. An expression representing a subset of individuals on which to perform analysis. e.g. sub=expression(sex==1).
可选的。一个表达式，表示个人的一个子集进行分析。例如sub=expression(sex==1)。
参数：adjust
a logical flag. If adjust=TRUE, the adjusted degrees of freedom is used. This is recommended when the computed degrees of freedom is larger than the complete data degrees of freedom. By default, adjust=FALSE.
一个逻辑标志。如果调整= TRUE，调整后的自由度。当所计算的自由度是大于完整的数据的自由度，这是推荐的。默认情况下，调整= FALSE。
值----------Value----------
haplo.long returns an object of class hapLong.
haplo.long返回一个对象类hapLong。
The summary function can be used to obtain and print a summary of the results.
summary函数可以用来获取和打印结果的摘要。
An object of class hapLong is a list containing the following components:
一个对象的类hapLong的是一个列表，其中包含以下组件：
参数：fixed_formula
fixed effects formula.
固定效应公式。
参数：random_formula
random effects formula.
随机效应公式。
参数：results
a table containing the coefficients, averaged over the sim models performed; standard errors, computed as the sum of the between-imputation and within-imputation variance; and p-values, based on a t-distribution with appropriately computed degrees of freedom, of the parameter estimates.
一个表，其中包含的系数，平均sim模型;标准误差，计算的总和之间的归集，归集内方差;和p值，在t分布的适当的计算度自由，参数估计。
参数：empiricalResults
a list containing the coefficients, standard errors and p-values calculated at each simulation.
一个列表，包含在每个模拟计算的系数，标准误差和p值。
参数：ANOD
analysis of deviance table for the fitted model.
分析拟合模型的偏差表。
参数：logLik
the log-likelihood for the fitted model.
对数似然的拟合模型。
参数：AIC
Akaike Information Criterion for the linear model fit using formula.
赤池信息准则的线性模型拟合公式。
参数：aicEmpirical
Akaike Information Criteria calculated at each simulation.
在每个仿真计算的Akaike信息准则。
参数：corStruct
correlation structure used in the fitted model.
相关结构拟合模型。
参数：effect
the haplotypic effect modelled, "ADDITIVE", "DOMINANT" or "RECESSIVE"
单倍型效果为蓝本，“添加剂”，“显性”或“隐性”
注意----------Note----------
To model a codominant haplotypic effect, define the desired haplotype as a factor in the formula1 argument. e.g. factor(h.AAA), and use the default option for effect
要对一个显性单倍型的效果，定义所需的单倍型的一个因素formula1参数。例如factor(h.AAA)，并使用默认选项为effect
（作者）----------Author(s)----------
Pamela A. McCaskie
参考文献----------References----------
参见----------See Also----------
snp.long, haplo.quant, haplo.quant, haplo.long
snp.long，haplo.quant，haplo.quant，haplo.long
实例----------Examples----------
data(SNPlong.dat)
# convert SNP.dat to format required by infer.haplos[SNP.dat转换，格式化所需的infer.haplos]
longHaplo.dat <- SNP2Haplo(SNPlong.dat)
data(longPheno.dat)
# generate haplotype frequencies and haplotype design matrix[产生单倍型频率和单倍型设计矩阵]
myinfer<-infer.haplos(longHaplo.dat)
# print haplotype frequencies generated by infer.haplos[打印单倍型频率所产生的infer.haplos]
myinfer$hap.freq
# generate haplo object where haplotypes with a frequency[单倍型的频率产生单倍体对象]
# below min.freq are grouped as a category called "rare"[下面min.freq分为一类被称为“罕见”]
myhaplo<-make.haplo.rare(myinfer,min.freq=0.05)
mymodel <- haplo.long(fixed=fev1f~h.ACV2, random=~1|ID,
pheno=longPheno.dat, haplo=myhaplo, cor="corCAR1",
form=~year|ID, sim=10)
summary(mymodel)
# example with a subsetting variable - looking at males only[例如，一个子集的变量 - 只在男性]
mymodel <- haplo.long(fixed=fev1f~height+h.ACV2, random=~1|ID,
pheno=longPheno.dat, haplo=myhaplo, cor="corCAR1",
form=~year|ID, sim=10, sub=expression(sex==1))
summary(mymodel)
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 2012-9-30 02:46:29
