R/updateE.R

In FRASER: Find RAre Splicing Events in RNA-Seq Data

#'
#' Update E step for the autoencoder fit
#'
#' @noRd
updateE <- function(fds, control, BPPARAM, verbose){
    par <- as.vector(E(fds))
    D <- D(fds)
    k <- K(fds)
    n <- N(fds)
    x <- x(fds, noiseAlpha=currentNoiseAlpha(fds))
    b <- b(fds)
    rho <- rho(fds)
    
    control[['maxit']] <- 50
    
    fit <- optim(par, fn=truncNLL_e, gr=truncGrad_e,
                    x=as.matrix(x), D=D, k=as.matrix(k), n=as.matrix(n), 
                    rho=rho, b=b, method="L-BFGS-B", control=control)
    
    # Check that fit converged
    if(isTRUE(verbose) & fit$convergence != 0){
        print(paste('Update E did not converge: ', fit$message))
    }
    
    # update ods
    E(fds) <- fit$par
    
    return(fds)
}