seqMetaExample: Example data for illustrating seqMeta

In seqMeta: Meta-Analysis of Region-Based Tests of Rare DNA Variants

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

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"=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)

Example output

Loading required package: survival
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog

seqMeta documentation built on May 2, 2019, 10:59 a.m.