Description Usage Arguments Value Author(s) References Examples
It gives p-values of the MTSPUsSet tests and MTaSPUsSet test with GWAS summary statistics.
1 2 3 4 5 6 7 8 9 10 | MTaSPUsSet(
Zs,
corSNP,
corPhe,
pow = c(1, 2, 4, 8),
pow2 = c(1, 2, 4, 8),
n.perm = 5000,
Ps = FALSE,
prune = TRUE
)
|
Zs |
Z-score matrix. row represent SNPs and column represent traits. 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). |
corPhe |
Correlation matirx of phenotypes to be tested; Estimated from Z-scores. |
pow |
SNP specific power(gamma values) used in MTSPUsSet test. |
pow2 |
GENE specific power(gamma values) used in MTSPUsSet test. |
n.perm |
number of permutations or bootstraps. |
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. |
A vector object, MTSPUsSet test P values and MTaSPUsSet P value.
Il-Youp Kwak and Wei Pan
Il-Youp Kwak, Wei Pan (2017) Gene- and pathway-based association tests for multiple traits with GWAS summary statistics, Bioinformatics, 33(1), 64-71.
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