From 8eb24b5c09bec850c1ad47180e3c89790f672f37 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Fri, 8 Dec 2023 13:34:01 +1100
Subject: [PATCH] add size factor to glmmseq

---
 R/functions.R    | 5 +++++
 R/functions_SE.R | 5 +++++
 2 files changed, 10 insertions(+)

diff --git a/R/functions.R b/R/functions.R
index 0ee421de..ed5d0087 100755
--- a/R/functions.R
+++ b/R/functions.R
@@ -779,11 +779,16 @@ get_differential_transcript_abundance_glmmSeq <- function(.data,
   # Make sure the order matches the counts
   dispersion = dispersion[rownames(counts)]
 
+  # Scaling
+  sizeFactors <- counts |> edgeR::calcNormFactors(method = scaling_method)
+  
+  
   glmmSeq_object =
     glmmSeq( .formula,
           countdata = counts ,
           metadata =   metadata,
           dispersion = dispersion,
+          sizeFactors = sizeFactors,
           progress = TRUE,
           method = method |> str_remove("(?i)^glmmSeq_"),
           ...
diff --git a/R/functions_SE.R b/R/functions_SE.R
index a9c087fa..557cb5e4 100755
--- a/R/functions_SE.R
+++ b/R/functions_SE.R
@@ -1154,11 +1154,16 @@ get_differential_transcript_abundance_glmmSeq_SE <- function(.data,
   # Make sure the order matches the counts
   dispersion = dispersion[rownames(counts)]
 
+  # Scaling
+  sizeFactors <- counts |> edgeR::calcNormFactors(method = scaling_method)
+  
+  
   glmmSeq_object =
     glmmSeq( .formula,
                       countdata = counts ,
                       metadata =   metadata |> as.data.frame(),
                       dispersion = dispersion,
+             sizeFactors = sizeFactors,
                       progress = TRUE,
                       method = method |> str_remove("(?i)^glmmSeq_" ),
                       ...