Description Usage Arguments Value Author(s) References See Also Examples
It gives p-values of the SPUsPath tests and aSPUsPath test with GWAS summary statistics.
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Zs |
Z-scores for each SNPs. It could be P-values if the Ps option is TRUE. |
corSNP |
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. |
prune |
if it is TRUE, do pruing before the test using pruneSNP function. |
P-values for SPUMpath tests and aSPUMpath test.
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
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