Merge pull request #311 from stemangiola/fix-interactions-for-DE

Fix interactions for de

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidybulk
 Title: Brings transcriptomics to the tidyverse 
-Version: 1.15.5
+Version: 1.15.6
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",

R/functions.R

@@ -465,6 +465,12 @@ get_differential_transcript_abundance_bulk <- function(.data,
 			data = df_for_edgeR %>% select(!!.sample, one_of(parse_formula(.formula))) %>% distinct %>% arrange(!!.sample)
 		)
 
+	# Replace `:` with ___ because it creates error with edgeR
+	if(design |> colnames() |> str_detect(":") |> any()) {
+	  message("tidybulk says: the interaction term `:` has been replaced with `___` in the design matrix, in order to work with edgeR.")
+	  colnames(design) = design |> colnames() |> str_replace(":", "___") 
+	}
+
 	# Print the design column names in case I want contrasts
 	message(
 		sprintf(

R/functions_SE.R

@@ -741,6 +741,12 @@ get_differential_transcript_abundance_bulk_SE <- function(.data,
 			data = sample_annotation
 		)
 
+	# Replace `:` with ___ because it creates error with edgeR
+	if(design |> colnames() |> str_detect(":") |> any()) {
+	  message("tidybulk says: the interaction term `:` has been replaced with `___` in the design matrix, in order to work with edgeR.")
+	  colnames(design) = design |> colnames() |> str_replace(":", "___") 
+	}
+
 	# Print the design column names in case I want contrasts
 	message(
 		sprintf(

tests/testthat/test-bulk_methods_SummarizedExperiment.R

@@ -64,7 +64,6 @@ test_that("tidybulk SummarizedExperiment normalisation",{
 
 })
 
-
 test_that("quantile normalisation",{
 
   res = se_mini |> quantile_normalise_abundance()
@@ -109,7 +108,6 @@ test_that("quantile normalisation",{
 
 })
 
-
 test_that("tidybulk SummarizedExperiment normalisation subset",{
 
   res = se |> identify_abundant() |> scale_abundance(
@@ -124,10 +122,6 @@ test_that("tidybulk SummarizedExperiment normalisation subset",{
 
 })
 
-
-
-
-
 test_that("tidybulk SummarizedExperiment clustering",{
 
   res = cluster_elements(se, method="kmeans", centers = 2)
@@ -357,7 +351,6 @@ test_that("differential trancript abundance - SummarizedExperiment",{
 
 })
 
-
 test_that("differential trancript abundance - SummarizedExperiment - alternative .abundance",{
 
   assays(se_mini) = list(counts = assay(se_mini), bla = assay(se_mini))
@@ -437,6 +430,24 @@ test_that("differential trancript abundance - SummarizedExperiment - alternative
 
 })
 
+test_that("DE interaction effects", {
+
+  # Att interaction factor
+  col_data = colData(breast_tcga_mini_SE)
+  set.seed(42)
+  col_data$interaction_term = sample(c(0,1), size = nrow(col_data), replace = TRUE)
+  colData(breast_tcga_mini_SE) = col_data
+
+  breast_tcga_mini_SE |> 
+    identify_abundant(factor_of_interest = Call) |>
+    test_differential_abundance( 
+      ~ Call * interaction_term, 
+      contrasts = "CallHer2___interaction_term",
+      method="edgeR_quasi_likelihood" 
+    ) |> 
+    expect_no_error()
+
+})
 
 test_that("Voom with treat method",{
 
@@ -524,8 +535,6 @@ test_that("differential trancript abundance - random effects SE",{
 
 })
 
-
-
 test_that("filter abundant - SummarizedExperiment",{
 
   res =		keep_abundant(		se	)