[R] no solution yet, please help: extract p-value from mixed model in kinship package

From: Ram H. Sharma <sharma.ram.h_at_gmail.com>
Date: Fri, 15 Apr 2011 09:30:30 -0400


 I am making the question clear. Please help.

> Dear R experts
>
> I was using kinship package to fit mixed model with kinship matrix.
> The package looks like lme4, but I could find a way to extract p-value
> out of it. I need to extract is as I need to analyse large number of
> variables (> 10000).
>
> Please help me:
>
> require(kinship)
>
> #Generating random example data
>

> #********************pedigree data*****************************

id <- 1:100

dadid <- c(rep(0, 5), rep(1, 5), rep(3, 5), rep(5, 5), rep(7, 10), rep(9, 10), rep(11, 10), rep(13, 10), rep(15, 10), rep(17, 10), rep(19, 10), rep(21, 10))

momid <- c(rep(0, 5), rep(2, 5), rep(4, 5), rep(6, 5), rep(8, 10), rep(10, 10), rep(12, 10), rep(14, 10), rep(16, 10), rep(18, 10), rep(20, 10), rep(22, 10) )

ped <- data.frame(id, dadid, momid)

# *****************************kmatrix**************************************

> cfam <- makefamid(ped$id,ped$momid, ped$dadid)
>
> kmat <- makekinship(cfam, ped$id, ped$momid, ped$dadid)
>
> #*****************************************x and y variables


> set.seed(3456)
>
> dat <- sample(c(-1,0,1), 10000, replace = TRUE)
>
> snpmat<- data.frame(matrix(dat, ncol = 100))
>
> names(snpmat) <- c(paste ("VR",1:100, sep='' ))
>
> yvar <- rnorm(100, 30, 5)
> covtrait <- rnorm(100, 10, 5)
>
> mydata <- data.frame(id, yvar, covtrait, snpmat)
>

#******************************mixed model in lmekin
*******************************************

>
> fmod <- lmekin(yvar ~ mydata[,3] , data= mydata, random = ~1|id,
> varlist=list(kmat)) $coefficients[2,4] # does not work
>
> # **************************************error
> message********************************************

> Error message:

Error in lmekin(yvar ~ mydata[, 3], data = mydata, random = ~1 | id, varlist = list(kmat))$coefficients[2, :
  incorrect number of dimensions
In addition: Warning message:
In coxme.varcheck(ncluster, varlist, n, gvars, groups, sparse, rescale, :   Diagonal of variance matrix is not constant

#**************************************ultimate target: to put in
loop*******************************

> Ultimately I want to put into the loop:
>
> for(i in 3:length(mydata)) {
>
> P <- vector (mode="numeric", length = 1000)
>
> P[i] <- lmekin(yvar~ mydata[,i] , data= mydata, random = ~1|id,
> varlist=list(kmat)) $coefficients[2,4]
>
> }
>

> Same errors: I tried lme4 conventioned but did not work !

> I can extract fixed effects as well as I do in lme4
> b <- fixef(fit1)
>

> Error in UseMethod("fixef") :
> no applicable method for 'fixef' applied to an object of class "lmekin"
>
>
> --
>
> Ram H
>

-- 

Ram H

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Received on Fri 15 Apr 2011 - 15:53:40 GMT

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