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 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.