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] #...