Merge pull request #296 from stemangiola/glmmTMB

add method glmmTMB
stemangiola · Sep 17, 2023 · be98005 · be98005
2 parents 543c7ee + a02224b
commit be98005
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Showing 9 changed files with 444 additions and 41 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -83,6 +83,7 @@ Suggests:
     pbapply,
     pbmcapply,
     lme4,
+    glmmTMB,
     MASS
 VignetteBuilder: 
     knitr

diff --git a/NAMESPACE b/NAMESPACE
@@ -172,6 +172,7 @@ importFrom(stats,median)
 importFrom(stats,model.matrix)
 importFrom(stats,na.omit)
 importFrom(stats,p.adjust)
+importFrom(stats,pchisq)
 importFrom(stats,plogis)
 importFrom(stats,prcomp)
 importFrom(stats,qlogis)

diff --git a/R/functions.R b/R/functions.R
@@ -783,7 +783,7 @@ get_differential_transcript_abundance_glmmSeq <- function(.data,
   )
 
   glmmSeq_object |>
-    summary() |>
+    summary_lmmSeq() |>
     as_tibble(rownames = "gene") |>
     mutate(across(starts_with("P_"), list(adjusted = function(x) p.adjust(x, method="BH")), .names = "{.col}_{.fn}")) |>
 

diff --git a/R/functions_SE.R b/R/functions_SE.R
@@ -1158,7 +1158,7 @@ get_differential_transcript_abundance_glmmSeq_SE <- function(.data,
     )
 
   glmmSeq_object |>
-    summary() |>
+    summary_lmmSeq() |>
     as_tibble(rownames = "transcript") |>
     mutate(across(starts_with("P_"), list(adjusted = function(x) p.adjust(x, method="BH")), .names = "{.col}_{.fn}")) |>