R: Pathway based Sum of Powered Score tests (SPUsPath) and...
aSPUsPath
R Documentation
Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics.
Description
It gives p-values of the SPUsPath tests and aSPUsPath test with GWAS summary statistics.
Z-scores for each SNPs. It could be P-values if the Ps option is TRUE.
corrSNP
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).
pow
SNP specific power(gamma values) used in SPUpath test.
pow2
GENE specific power(gamma values) used in SPUpath test.
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.
n.perm
number of permutations.
Ps
TRUE if input is p-value, FALSE if input is Z-scores. The default is FALSE.
Value
P-values for SPUMpath tests and aSPUMpath test.
Author(s)
Il-Youp Kwak and Wei Pan
References
Il-Youp Kwak, Wei Pan (2015)
Adaptive Gene- and Pathway-Trait Association Testing with GWAS Summary Statistics,
Bioinformatics, doi: 10.1093/bioinformatics/btv719