minor version bump

MarioniLab · Apr 30, 2024 · f1bb7f0 · f1bb7f0
1 parent bcbb438
commit f1bb7f0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: miloR
 Type: Package
 Title: Differential neighbourhood abundance testing on a graph
-Version: 1.99.15
+Version: 1.99.16
 Authors@R:
     c(person("Mike", "Morgan", role=c("aut", "cre"), email="michael.morgan@abdn.ac.uk",
      comment=c(ORCID="0000-0003-0757-0711")),

diff --git a/R/testNhoods.R b/R/testNhoods.R
@@ -526,8 +526,8 @@ testNhoods <- function(x, design, design.df, kinship=NULL,
         rownames(res) <- 1:length(fit)
         colnames(res)[6:(6+length(rand.levels)-1)] <- paste(names(rand.levels), "variance")
     } else {
-
-        fit <- glmQLFit(dge, x.model, robust=robust)
+        # need to use legacy=TRUE to maintain original edgeR behaviour
+        fit <- glmQLFit(dge, x.model, robust=robust, legacy=TRUE)
         if(!is.null(model.contrasts)){
             mod.constrast <- makeContrasts(contrasts=model.contrasts, levels=x.model)
             res <- as.data.frame(topTags(glmQLFTest(fit, contrast=mod.constrast),

diff --git a/vignettes/milo_contrasts.Rmd b/vignettes/milo_contrasts.Rmd
@@ -99,7 +99,7 @@ contrast.1 <- c("Age1wk - Age4wk") # the syntax is <VariableName><ConditionLevel
 
 # we need to use the ~ 0 + Variable expression here so that we have all of the levels of our variable as separate columns in our model matrix
 da_results <- testNhoods(thy.milo, design = ~ 0 + Age, design.df = thy.design, model.contrasts = contrast.1,
-                         fdr.weighting="graph-overlap")
+                         fdr.weighting="graph-overlap", norm.method="TMM")
 table(da_results$SpatialFDR < 0.1)
 ```