search for: snpmat

Displaying 3 results from an estimated 3 matches for "snpmat".

2011 Apr 15
1
no solution yet, please help: extract p-value from mixed model in kinship package
...m <- 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) > #******************************mix...
2011 Jul 27
1
SNP Tables
Hello, I have indicators for the present of absent of a snps in columns and the categorey (case control column). I would like to extract ONLY the tables and the indices (SNPS) that give me 2 x 3 tables. Some gives 2x 2 tables when one of the allelle is missing. The data look like the matrix snpmat below: so the first snp should give me the following table: (aa=0, Aa=1 and AA=2) aa Aa AA case 2 3 0 control 2 2 0 So I should not use this one or if I am using it, then I need to see 0 0 in to AA column which I don...
2011 Apr 14
0
extract p-value from mixed model in kinship package
..., 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] #...