aSPUw {aSPU} | R Documentation |

## 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.

### Author(s)

Il-Youp Kwak, Junghi Kim and Wei Pan

### 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

### Examples

```
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)
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.
```

*aSPU*version 1.50 Index]