Updated formula

biobakery · Jul 10, 2024 · d07fd88 · d07fd88
1 parent c2327d6
commit d07fd88
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MTXmodel
 Title: Statistical approaches for differential expression analysis in metatranscriptomics
 Year: 2021
-Version: 1.2.4
+Version: 1.2.5
 Authors@R: c(
   person("Yancong", "Zhang", email = "[email protected]", role = "aut"), 
   person("Eric", "Franzosa", email = "[email protected]", role = c("aut", "cre"))

diff --git a/NEWS b/NEWS
@@ -1,6 +1,9 @@
 
 # MTXmodel History #
 
+## Changes in v1.2.5 (2024-07-10) ##
+* Tweaked formula
+
 ## Changes in v1.2.4 (2023-09-07) ##
 * Fixed xtfrm warning message
 * Add log info if there is no result

diff --git a/R/utility_ext.R b/R/utility_ext.R
@@ -409,8 +409,7 @@ fit.each <- function(
 
         mydf <- data.frame(expr = features[,i], mymeta)
         formula_text <-
-            paste("expr ~ ", paste(colnames(mymeta), collapse = " + "))
-        #logging::loginfo("Formula for fixed effects: %s", formula_text)
+            paste("expr ~ ", paste(c(fixed_effects, i), collapse = " + "))
         formula <-
             tryCatch(
                 as.formula(formula_text),
@@ -539,7 +538,7 @@ fit.dnadata <-
             model,
             fixed_effects,
             effects_names,
-            random_effects_formula = NULL)
+            random_effects_formula)
 
 
         # bind the results for each feature

diff --git a/test/demo_output/all_results.tsv b/test/demo_output/all_results.tsv
diff --git a/test/demo_output/fitted.rds b/test/demo_output/fitted.rds
diff --git a/test/demo_output/mtx_model.log b/test/demo_output/mtx_model.log
diff --git a/test/demo_output/ranef.rds b/test/demo_output/ranef.rds
diff --git a/test/demo_output/residuals.rds b/test/demo_output/residuals.rds
diff --git a/test/demo_output/significant_results.tsv b/test/demo_output/significant_results.tsv