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

?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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