Response or phenotype data. It can be a disease indicator; =0 for controls, =1 for cases.
Or it can be a quantitative trait. A vector with length n (number of observations).
X
Genotype or other data; each row for a subject, and each column
for an SNP (or a predictor). The value of each SNP is the # of the copies
for an allele. A matrix with dimension n by k (n : number of observation, k : number of SNPs (or predictors) ).
cov
Covariates. A matrix with dimension n by p (n :number of observation, p : number of covariates).
model
Use "gaussian" for a quantitative trait, and use "binomial" for a binary trait.
snp.info
SNP information matrix, the 1st column is SNP id, 2nd column is chromosome #, 3rd column indicates SNP location.
gene.info
GENE information matrix, The 1st column is GENE id, 2nd column is chromosome #, 3rd and 4th column indicate start and end positions of the gene.
pow
SNP specific power(gamma values) used in SPUpath test.
pow2
GENE specific power(gamma values) used in SPUpath test.
n.perm
number of permutations.
usePCs
indicating whether to extract PCs and then use PCs of X.
varprop
the proportion of the variations explained (cutoff) that
determines how many top PCs to use.
Value
P-values for SPUpath tests and aSPUpath test.
Author(s)
Il-Youp Kwak and Wei Pan
References
Wei Pan, Il-Youp Kwak and Peng Wei (2015)
A Powerful and Pathway-Based Adaptive Test for Genetic Association With Common or Rare Variants, The American Journal of Human Genetics, 97, 86-98
See Also
simPathAR1Snp
Examples
## Not run: dat1<-simPathAR1Snp(nGenes=20, nGenes1=5, nSNPlim=c(1, 20),
nSNP0=1, LOR=.2, n=100, MAFlim=c(0.05, 0.4), p0=0.05 )
## End(Not run)
# p-values of SPUpath and aSPUpath tests.
## Not run: p.pathaspu<- aSPUpath(dat1$Y, dat1$X, snp.info = dat1$snp.info,
gene.info = dat1$gene.info,
model = "binomial", pow=1:8, pow2=c(1, 2, 4, 8), n.perm=1000)
## End(Not run)
p.pathaspu
## pow = 1:8 and pow2 = 1,2,4,8
## So, there are 8*4 = 32 SPUpath p-values.
## SPUpathi,j corresponds pow = i , pow2 = j
## The last element, aSPUpath gives aSPUpath p-value.