R: gene-Multitrait Sum of Powered Score (MTSPUsSetScore) tests...
MTaSPUsSetScore
R Documentation
gene-Multitrait Sum of Powered Score (MTSPUsSetScore) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics. (Score version added)
Description
It gives p-values of the MTSPUsSet tests MTScore and MTaSPUsSet_Score test with GWAS summary statistics.
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 MTSPUsSetScore test.
pow2
GENE specific power(gamma values) used in MTSPUsSetScore 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.
Value
A vector object, MTSPUsSet test, MTScore test P values and MTaSPUsSet_Score P value.
Author(s)
Il-Youp Kwak and Wei Pan
References
Il-Youp Kwak, Wei Pan (2016)
Gene- and pathway-based association tests for multiple
traits with GWAS summary statistics