Ram H. Sharma
2011-Apr-14 03:38 UTC
[R] extract p-value from mixed model in kinship package
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 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) cfam <- makefamid(ped$id,ped$momid, ped$dadid) kmat <- makekinship(cfam, ped$id, ped$momid, ped$dadid) set.seed(3456) SNPdata <- c(1:1000) 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) mydata <- data.frame(trait1, covtrait, snpmat) fmod <- lmekin(y~ mydata[,i] , data= snpdata, random = ~1|id, varlist=list(kmat)) $coefficients[2,4] # does not work Ultimately I want to put into the loop: for(i in 3:length(snpdata)) { P <- vector (mode="numeric", length = 1000) P[i] <- lmekin(trait1~ snpdata[,i] , data= snpdata, random = ~1|id, varlist=list(kmat)) $coefficients[2,4] } Error message: incorrect number of dimensions 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