aSPUs {aSPU}R Documentation

Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics.


It gives p-values of the SPUs tests and aSPUs test with GWAS summary statistics.


aSPUs(Zs, corSNP, pow = c(1:8, Inf), n.perm = 1000, Ps = FALSE, prune = TRUE)



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


Correlation matirx of the SNPs to be tested; estimated from a reference panel (based on the same set of the reference alleles as used in calculating Z-scores).


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


number of permutations or bootstraps.


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


if it is TRUE, do pruing before the test using pruneSNP function.


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 SPUs and aSPUs tests.


Il-Youp Kwak and Wei Pan


Il-Youp Kwak, Wei Pan (2015) Adaptive Gene- and Pathway-Trait Association Testing with GWAS Summary Statistics, Bioinformatics, 32(8), 1178-1184.

See Also

aSPUw aSPU aSPUsPath


## example analysis using aSPUM test.
g <- kegg9$[1,1]  #  SOAT1 
## Take snps mapped on gene "SOAT1" from the information of and 
snps <- which( ( kegg9$[,2] == kegg9$[kegg9$[,1] == g, 2] ) &
                 (kegg9$[,3] > kegg9$[kegg9$[,1] == g, 3] ) &
                 (kegg9$[,3] < kegg9$[kegg9$[,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 <- aSPUs(newP, corSNP=ldsub , pow=c(1:8, Inf), n.perm=100, Ps=TRUE)

# This is a vector of Test Statistics for SPUM and aSPUM tests.
# SPUs1 to SPUsInf corresponds with the option pow=c(1:8, Inf)
# They are SPUs test statistics.
# The last element aSPUs is minimum of them, aSPUs statistic.

# This is a vector of p-values for SPUs and aSPUs tests.
# SPUs1 to SPUsInf corresponds with the option pow=c(1:8, Inf)
# They are p-values for corresponding SPUs tests.
# The last element is p-value of aSPUs test.

[Package aSPU version 1.50 Index]