| em_hmm {ReAD} | R Documentation |
EM algorithm in combination with a non-parametric algorithm for estimation of the rLIS statistic.
Description
Estimate the rLIS values accounting for the linkage disequilibrium across two genome-wide association studies via the four-state hidden Markov model. Apply a step-up procedure to control the FDR of replicability null.
Usage
em_hmm(pa_in, pb_in, pi0a_in, pi0b_in)
Arguments
pa_in |
A numeric vector of p-values from study 1. |
pb_in |
A numeric vector of p-values from study 2. |
pi0a_in |
An initial estimate of the null probability in study 1. |
pi0b_in |
An initial estimate of the null probability in study 2. |
Value
rLIS |
The estimated rLIS for replicability null. |
fdr |
The adjusted values based on rLIS for FDR control. |
loglik |
The log-likelihood value with converged estimates of the unknowns. |
pi |
An estimate of the stationary probabilities of four states (0,0), (0,1), (1,0), (1,1). |
A |
An estimate of the 4-by-4 transition matrix. |
f1 |
A non-parametric estimate for the non-null probability density function in study 1. |
f2 |
A non-parametric estimate for the non-null probability density function in study 2. |