add size factor to glmmseq

stemangiola · Dec 8, 2023 · 8eb24b5 · 8eb24b5
1 parent 11607be
commit 8eb24b5
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diff --git 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
@@ -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_" ),
                       ...