estcov
(Package: aSPU) :
estcov
Estimate the covariance matrix of multiple traits based on their (null) summary Z-scores.
● Data Source:
CranContrib
● Keywords:
● Alias: estcov
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simPathAR1Snp
(Package: aSPU) :
Simulating a pathway with multiple SNPs.
It gives a simulated SNPs consisting of multiple genes in a pathway. Each SNPs from a latent multivariate Gaussian variable with an AR1 correlation structure.
● Data Source:
CranContrib
● Keywords:
● Alias: simPathAR1Snp
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GEEaSPU
(Package: aSPU) :
The SPU and aSPU tests for multiple traits - single SNP association in generalized estimating equations.
It gives p-values of the GEESPU tests and GEEaSPU test.
● Data Source:
CranContrib
● Keywords:
● Alias: GEEaSPU
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MTaSPUsSetPath
(Package: aSPU) :
Multitraits - Pathway based Sum of Powered Score tests (MTSPUsSetPath) and adaptive MTSPUsSetpath (MTaSPUsSetPath) test for multi trait - pathway association with GWAS summary statistics.
It gives p-values of the MTSPUsSetPath tests and MTaSPUsSetPath test with GWAS summary statistics.
● Data Source:
CranContrib
● Keywords:
● Alias: MTaSPUsSetPath
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GATES2
(Package: aSPU) :
Gene-based Association Test that uses an extended Simes procedure (GATES) for single trait - SNP set association
Get the p-value of GATES. Usually it is used to get genomewise p-values. This function is taken from postgwas package. There is a little modification of the code GATES in postgwas package. 1) The approximated matrix may have negative eigen value, we modified it not to have negative values; 2) we added one more return (the key gene location) for Hyst method.
● Data Source:
CranContrib
● Keywords:
● Alias: GATES2
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aSPU
(Package: aSPU) :
Sum of Powered Score (SPU) tests and adaptive SPU (aSPU) test for single trait - SNP set association.
It gives p-values of the SPU tests and aSPU test.
● Data Source:
CranContrib
● Keywords:
● Alias: aSPU
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minP
(Package: aSPU) :
minP test.
Return exact minP test p-value for multiple traits - single SNP association.
● Data Source:
CranContrib
● Keywords:
● Alias: minP
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aSPUpath
(Package: aSPU) :
Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association.
It gives p-values of the SPUpath tests and aSPUpath test.
● Data Source:
CranContrib
● Keywords:
● Alias: aSPUpath
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aSPUsPath
(Package: aSPU) :
Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics.
It gives p-values of the SPUsPath tests and aSPUsPath test with GWAS summary statistics.
● Data Source:
CranContrib
● Keywords:
● Alias: aSPUsPath
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MTaSPUsSetScore
(Package: aSPU) :
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)
It gives p-values of the MTSPUsSet tests MTScore and MTaSPUsSet_Score test with GWAS summary statistics.
● Data Source:
CranContrib
● Keywords:
● Alias: MTaSPUsSetScore
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