seqMeta (version 1.6.7)

seqMetaExample:

Example data for illustrating seqMeta

Description

Contains simulated data for two cohorts. See the example for the exact code used to generate the data.

Usage

data(seqMetaExample)

Format

This contains simulated data for two cohorts to illustrate seqMeta package

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"=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)