diff --git a/R/testNhoods.R b/R/testNhoods.R index 71b1ac8..239595c 100644 --- a/R/testNhoods.R +++ b/R/testNhoods.R @@ -419,6 +419,13 @@ testNhoods <- function(x, design, design.df, kinship=NULL, # I think these need to be logged offsets <- log(dge$samples$norm.factors) + + # if glmm.solver isn't set but is running GLMM + if(is.null(glmm.solver) & isTRUE(is.lmm)){ + warning("NULL value for glmm.solver - setting to Fisher. Please set glmm.solver") + glmm.solver <- "Fisher" + } + glmm.cont <- list(theta.tol=max.tol, max.iter=max.iters, solver=glmm.solver) #wrapper function is the same for all analyses