Last data update: 2014.03.03
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R: example Data for illustrating skatMeta
skatExample | R Documentation |
example Data for illustrating skatMeta
Description
Contains simulated data for two cohorts. See the example for the exact code used to generate the data.
Usage
data(skatExample)
Format
This contains simulated data for two cohorts to illustrate skatMeta package
Z1 ,Z2 -
Genotype matrices for cohorts 1 and 2 respectively
pheno1 ,pheno2 -
phenotype matrices for cohorts 1 and 2 respectively
- kins
-
The kinship matrix for cohort 2
Examples
#Data generated by
## Not run:
set.seed(20)
n <- 600 #observations per cohort
d <- 2000 #SNPs
k <- 100 #genes
##### First cohort of unrelated individuals:
Z1 <- replicate(d,rbinom(n,2,rbeta((n),3,200)))
## assign SNP id's to the columns
colnames(Z1) <- sample(d+50,d) + 1e6
pheno1 <- data.frame("y" = rnorm(n), "sex"=rep(1:2,(n/2)), "bmi"=rnorm(n,25,2),
"ybin" = rbinom(n,1,.5), "time"=rpois(n,5), "status"=rbinom(n,1,.9))
genes <- paste0("gene",1:k)
SNPInfo <- data.frame("Name" =1:(d+50) + 1e6, "gene" = sort(sample(genes,d+50,replace=T)))
#####Second cohort of family data:
# 150 families of size 4
require(kinship2)
fullped<-data.frame(famid=rep(1:(n/4),each=4),id=10001:(10000+n),fa=rep(0,n),mo=rep(0,n))
fullped$fa[(1:(n/4))*4-1]<-fullped$fa[(1:(n/4))*4]<-(1:(n/4))*4+9997
fullped$mo[(1:(n/4))*4-1]<-fullped$mo[(1:(n/4))*4]<-(1:(n/4))*4+9998
kins = makekinship(fullped$famid, fullped$id, fullped$fa, fullped$mo)
## generate a phenotype with 20% `heritability':
pheno2<-data.frame("id"=10001:(10000+n),"y"=t(rnorm(n)%*%chol(0.2*2*as.matrix(kins) +
0.8*diag(n))),"sex"=rep(1:2,(n/2)),"bmi"=rnorm(n,25,2))
Z2 <- replicate(d,rbinom(n,2,rbeta((n/4),3,200)[fullped$famid]))
colnames(Z2) <- sample(d+50,d) + 1e6
## End(Not run)
Results
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