Description Usage Arguments Details Value Author(s) References See Also Examples
Hypothesis testing for pleiotropy.
1 | pTest( fit, fitH0, vDigit=1000 )
|
fit |
Fit of the GPA model of interest. |
fitH0 |
GPA model fit under the null hypothesis of pleiotropy test. |
vDigit |
Number of digits for reporting parameter estimates and standard errors. For example, setting it to 1000 means printing out values up to three digits below zero. |
pTest
implements the hypothesis testing for pleiotropy.
It requires two GPA model fits, one of interest and one under the null hypothesis
(obtained by setting pleiotropyH0=TRUE
when running GPA
function),
and evaluates genetical correlation among multiple phenotypes using the likelihood ratio test.
Returns a list with components:
pi |
pi estimates. |
piSE |
Standard errors for pi estimates. |
statistics |
Statistics of the pleiotropy test. |
pvalue |
p-value of the pleiotropy test. |
Dongjun Chung
Chung D*, Yang C*, Li C, Gelernter J, and Zhao H (2014), "GPA: A statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data," PLoS Genetics, 10: e1004787. (* joint first authors)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## Not run:
# GPA without annotation data
fit.GPA.noAnn <- GPA( pmat, NULL )
# GPA under the null hypothesis of pleiotropy test
fit.GPA.pleiotropy.H0 <- GPA( pmat, NULL, pleiotropyH0=TRUE )
# hypothesis testing for pleiotropy
test.pleiotropy <- pTest( fit.GPA.noAnn, fit.GPA.pleiotropy.H0 )
## End(Not run)
|
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