R: Multitraits - Pathway based Sum of Powered Score tests...
MTaSPUsSetPath
R Documentation
Multitraits - Pathway based Sum of Powered Score tests (MTSPUsSetPath) and adaptive MTSPUsSetpath (MTaSPUsSetPath) test for multi trait - pathway association with GWAS summary statistics.
Description
It gives p-values of the MTSPUsSetPath tests and MTaSPUsSetPath 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.
corPhe
Correlation matirx of phenotypes to be tested; Estimated from Z-scores.
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).
pow1
SNP specific power(gamma values) used in MTSPUsSetPath test.
pow2
GENE specific power(gamma values) used in MTSPUsSetPath test.
pow3
Trait specific power(gamma values) used in MTSPUsSetPath 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 MTSPUsSetpath tests and MTaSPUsSetpPath test.
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