Description Usage Arguments Details Value Author(s) References See Also Examples
This function implements the method of Markitsis and Lai (2010).
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p |
a numeric vector the p-values |
start.pi0 |
numeric scalar, starting value of pi0 for EM algorithm. |
thresh.censor |
numeric scalar, the threshold of censoring. If |
eps |
numeric scalar, maximum tolerable absolute difference of parameter estimates for successive iterations in the EM algorithm. |
niter |
numeric scalar, maximum number of EM iterations. |
verbose |
logical scalar, indicating whether excessive outputs will be printed during EM algorithm. |
This function is an improved version of the CBpi0
function available at http://home.gwu.edu/~ylai/research/CBpi0/CBpi0.txt, which
implements the censored (1-paramater beta)-uniform mixture model to a large number of p-values.
A numeric scalar, being the proportion pi0 of true null hypotheses. The result has a class 'CBUM', with the following attributes:
converged |
logical, convergence status. |
iter |
numeric, number of iterations. |
call |
the |
alpha |
estimated alpha parameter for the beta component. |
lfdr |
numeric vector estimated local false discovery rates, if |
thresh.censor |
the censoring threshold for p-values. |
Long Qu modified the code from Markitsis and Lai (2010).
Anastasios Markitsis and Yinglei Lai (2010) A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes. Bioinformatics 26(5):640-646.
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