aSPU (version 1.50)

aSPUw: Inverse variance weighted Sum of Powered Score tests (SPUw) and adaptive SPUw (aSPUw) test for single trait - SNP set association.

Description

It gives the p-values of the SPUw tests and aSPUw test based on the permutations of the residuals or simulations from the null distripution.

Usage

aSPUw(
  Y,
  X,
  cov = NULL,
  resample = c("perm", "boot", "sim"),
  model = c("gaussian", "binomial"),
  pow = c(1:8, Inf),
  n.perm = 1000
)

Arguments

Y

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).

resample

Use "perm" for residual permutations, "sim" for simulations from the null distribution, and "boot" for parametric bootstrap.

model

Use "gaussian" for a quantitative trait, and use "binomial" for a binary trait.

pow

power used in SPU test. A vector of the powers.

n.perm

number of permutations or bootstraps.

Value

A list object, Ts : Test Statistics for the SPUw and aSPUw test. pvs : p-values for the SPUw and aSPUw test.

References

Junghi Kim, Jeffrey R Wozniak, Bryon A Mueller, Xiaotong Shen and Wei Pan (2014) Comparison of statistical tests for group differences in brain functional networks, Neuroimage, 1;101:681-694

See Also

aSPU

Examples

# NOT RUN {
data(exdat)

# increase n.perm for accurate p-value
# }
# NOT RUN {
out <- aSPUw(exdat$Y, exdat$X, pow = c(1:8, Inf), n.perm = 1000) 
# }
# NOT RUN {
out$Ts
# This is a vector of Test Statistics for SPU and aSPU tests.
# SPU1 to SPUInf corresponds with the option pow=c(1:8, Inf)
# They are SPU test statistics.
# The last element aSPU is minimum of them, aSPU statistic.

out$pvs
# This is a vector of p-values for SPU and aSPU tests.
# SPU1 to SPUInf corresponds with the option pow=c(1:8, Inf)
# They are p-values for corresponding SPU tests.
# The last element is p-value of aSPU test.

# }