seqMetaExample {seqMeta} | R Documentation |
Contains simulated data for two cohorts. See the example for the exact code used to generate the data.
data(seqMetaExample)
This contains simulated data for two cohorts to illustrate seqMeta package
Z1
,Z2
Genotype matrices for cohorts 1 and 2 respectively
pheno1
,pheno2
phenotype matrices for cohorts 1 and 2 respectively
The kinship matrix for cohort 2
#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"=as.character(1:(d+50) + 1e6), "gene"=sort(sample(genes,d+50,replace=T)), stringsAsFactors=FALSE) #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)