From 11607be2b77ae3f7711026379b77d755dcaf6ef1 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Fri, 8 Dec 2023 13:31:11 +1100
Subject: [PATCH] use lme4 to drop random effects

---
 R/functions_SE.R | 16 ++++++++--------
 R/utilities.R    | 29 -----------------------------
 2 files changed, 8 insertions(+), 37 deletions(-)

diff --git a/R/functions_SE.R b/R/functions_SE.R
index 23374aee..a9c087fa 100755
--- a/R/functions_SE.R
+++ b/R/functions_SE.R
@@ -1100,13 +1100,13 @@ get_differential_transcript_abundance_glmmSeq_SE <- function(.data,
     omit_contrast_in_colnames = FALSE
   }
 
-  # Check if package is installed, otherwise install
-  if (find.package("edgeR", quiet = TRUE) %>% length %>% equals(0)) {
-    message("tidybulk says: Installing edgeR needed for differential transcript abundance analyses")
-    if (!requireNamespace("BiocManager", quietly = TRUE))
-      install.packages("BiocManager", repos = "https://cloud.r-project.org")
-    BiocManager::install("edgeR", ask = FALSE)
-  }
+  # # Check if package is installed, otherwise install
+  # if (find.package("edgeR", quiet = TRUE) %>% length %>% equals(0)) {
+  #   message("tidybulk says: Installing edgeR needed for differential transcript abundance analyses")
+  #   if (!requireNamespace("BiocManager", quietly = TRUE))
+  #     install.packages("BiocManager", repos = "https://cloud.r-project.org")
+  #   BiocManager::install("edgeR", ask = FALSE)
+  # }
 
   # Check if package is installed, otherwise install
   if (find.package("glmmSeq", quiet = TRUE) %>% length %>% equals(0)) {
@@ -1136,7 +1136,7 @@ get_differential_transcript_abundance_glmmSeq_SE <- function(.data,
   # Create design matrix for dispersion, removing random effects
   design =
     model.matrix(
-      object = .formula |> eliminate_random_effects(),
+      object = .formula |> lme4::nobars(),
       data = metadata
     )
   
diff --git a/R/utilities.R b/R/utilities.R
index b59a58e0..1bf9cbe7 100755
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -1524,32 +1524,3 @@ feature__ =  get_special_column_name_symbol(".feature")
 sample__ = get_special_column_name_symbol(".sample")
 
 
-#' Produced using ChatGPT - Eliminate Random Effects from a Formula
-#'
-#' This function takes a mixed-effects model formula and returns a modified
-#' formula with all random effects removed, leaving only the fixed effects.
-#'
-#' @param formula An object of class \code{formula}, representing a mixed-effects model formula.
-#' @return A formula object with random effects parts removed.
-#' @examples
-#' eliminate_random_effects(~ age_days * sex + (1 | file_id) + ethnicity_simplified + assay_simplified + .aggregated_cells + (1 + age_days * sex | tissue))
-#' @noRd
-#' @importFrom stats as.formula
-eliminate_random_effects <- function(formula) {
-  # Convert the formula to a string
-  formula_str <- deparse(formula)
-  
-  # Split the string by '+' while keeping the brackets content together
-  split_str <- unlist(strsplit(formula_str, "(?<=\\))\\s*\\+\\s*|\\+\\s*(?=\\()", perl = TRUE))
-  
-  # Filter out the random effects parts
-  fixed_effects <- grep("\\|", split_str, value = TRUE, invert = TRUE)
-  
-  # Combine the fixed effects parts back into a single string
-  modified_str <- paste(fixed_effects, collapse = " + ")
-  
-  # Convert the modified string back to a formula
-  modified_formula <- as.formula(modified_str)
-  
-  return(modified_formula)
-}
\ No newline at end of file