aSPUM: Sum of Powered Score (SPU) tests and adaptive SPU (aSPU) test for meta-analyzed data.

Description

It gives p-values of the SPU tests and aSPU test for meta-analyzed data.

Usage

aSPUM(Zs, corrSNP, pow = c(1, 2, 4, 8, Inf), n.perm = 1000, Ps = FALSE)

Arguments

Z-scores for each SNPs. It could be P-values if the Ps option is TRUE.

corrSNP

Correaltion matirx of SNPs. Estimated from the reference population.

pow

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

n.perm

number of permutations or bootstraps.

TRUE if input is p-value, FALSE if input is Z-scores. The default is FALSE.

Value

A list object, Ts : test statistics for the SPU tests (in the order of the specified pow) and finally for the aSPU test. pvs : p-values for the SPU and aSPU tests.

References

Wei Pan, Junghi Kim, Yiwei Zhang, Xiaotong Shen and Peng Wei (2014) A powerful and adaptive association test for rare variants, Genetics, 197(4), 1081-95

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

Examples

Run this code

data(kegg9)
## example analysis using aSPUM test.
g <- kegg9$gene.info[1,1]  #  SOAT1
## Take snps mapped on gene "SOAT1" from the information of gene.info and snp.info.
snps <- which( ( kegg9$snp.info[,2] == kegg9$gene.info[kegg9$gene.info[,1] == g, 2] ) &
                 (kegg9$snp.info[,3] > kegg9$gene.info[kegg9$gene.info[,1] == g, 3] ) &
                 (kegg9$snp.info[,3] < kegg9$gene.info[kegg9$gene.info[,1] == g, 4] )  )
## Take subsets
newP <- kegg9$nP[snps] ;
ldsub <- kegg9$ldmatrix[snps, snps];
## Get p-value for gene SOAT1. Read vignette for details.
out <- aSPUM(newP, corrSNP=ldsub , pow=c(1,2,4,8, Inf), n.perm=100, Ps=TRUE)

out$Ts
# This is a vector of Test Statistics for SPUM and aSPUM tests.
# SPU1 to SPUInf corresponds with the option pow=c(1:8, Inf)
# They are SPU test statistics.
# The last element aSPUM is minimum of them, aSPUM statistic.

out$pvs
# This is a vector of p-values for SPUM and aSPUM tests.
# SPUM1 to SPUMInf corresponds with the option pow=c(1:8, Inf)
# They are p-values for corresponding SPUM tests.
# The last element is p-value of aSPUM test.