seqMetaExample: Example data, from seqMeta package

In bigQF: Quadratic Forms in Large Matrices

Description

Contains simulated data for two cohorts taken from the seqMeta package. The individual genes are too small for this to be a good use of the leading-eigenvalue approximation, but the data at least allow basic numerical comparisons.

Usage

data(seqMetaExample)

Format

This contains simulated data for two cohorts

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

Source

https://github.com/DavisBrian/seqMeta

Examples

data(seqMetaExample)

m<-coxme::lmekin(y~sex+bmi+(1|id),data=pheno2,varlist=2*kins,
	x=TRUE,y=TRUE,method="REML")

#first gene
g1snps<-c("1000001", "1000002", "1000003", "1000004", "1000005", "1000006", 
"1000007", "1000008", "1000009", "1000010", "1000012", "1000013", 
"1000014", "1000015")
Z2gene1<-Z2[,g1snps]

f<-famSKAT(Z2gene1, m, kins)
Q<-f$Q()
all.equal(Q, 56681.209)
## correct p is 0.742756401
pQF(Q,f,neig=4)

bigQF documentation built on Nov. 23, 2021, 5:06 p.m.