Merge pull request #318 from stemangiola/update_confounders_and_filtering

Update confounders and filtering

Author: stemangiola

R/methods.R

@@ -3132,6 +3132,7 @@ setGeneric("identify_abundant", function(.data,
 																		 .transcript = NULL,
 																		 .abundance = NULL,
 																		 factor_of_interest = NULL,
+																		 design = NULL,
 																		 minimum_counts = 10,
 																		 minimum_proportion = 0.7)
 	standardGeneric("identify_abundant"))
@@ -3142,6 +3143,7 @@ setGeneric("identify_abundant", function(.data,
 														.transcript = NULL,
 														.abundance = NULL,
 														factor_of_interest = NULL,
+														design = NULL,
 														minimum_counts = 10,
 														minimum_proportion = 0.7)
 {
@@ -3250,6 +3252,7 @@ setGeneric("identify_abundant", function(.data,
 	  edgeR::filterByExpr(
 	    min.count = minimum_counts,
 	    group = string_factor_of_interest,
+	    design = design,
 	    min.prop = minimum_proportion
 	  ) %>%
 	  not() |>
@@ -3345,6 +3348,7 @@ setGeneric("keep_abundant", function(.data,
 																			 .transcript = NULL,
 																			 .abundance = NULL,
 																			 factor_of_interest = NULL,
+																			 design = NULL,
 																			 minimum_counts = 10,
 																			 minimum_proportion = 0.7)
 	standardGeneric("keep_abundant"))
@@ -3355,6 +3359,7 @@ setGeneric("keep_abundant", function(.data,
 															.transcript = NULL,
 															.abundance = NULL,
 															factor_of_interest = NULL,
+															design = NULL,
 															minimum_counts = 10,
 															minimum_proportion = 0.7)
 {
@@ -3387,6 +3392,7 @@ setGeneric("keep_abundant", function(.data,
 			.transcript = !!.transcript,
 			.abundance = !!.abundance,
 			factor_of_interest = !!factor_of_interest,
+			design = design,
 			minimum_counts = minimum_counts,
 			minimum_proportion = minimum_proportion
 		) |>

R/methods_SE.R

@@ -1572,6 +1572,7 @@ setMethod("keep_variable",
 																 .transcript = NULL,
 																 .abundance = NULL,
 																 factor_of_interest = NULL,
+																 design = NULL,
 																 minimum_counts = 10,
 																 minimum_proportion = 0.7)
 {
@@ -1679,6 +1680,7 @@ setMethod("keep_variable",
 		edgeR::filterByExpr(
 			min.count = minimum_counts,
 			group = string_factor_of_interest,
+			design = design,
 			min.prop = minimum_proportion,
 			lib.size = Matrix::colSums(., na.rm=TRUE)
 		) %>%
@@ -1726,6 +1728,7 @@ setMethod("identify_abundant",
 														 .transcript = NULL,
 														 .abundance = NULL,
 														 factor_of_interest = NULL,
+														 design = NULL,
 														 minimum_counts = 10,
 														 minimum_proportion = 0.7)
 {
@@ -1745,7 +1748,8 @@ setMethod("identify_abundant",
 			factor_of_interest = !!factor_of_interest,
 			minimum_counts = minimum_counts,
 			minimum_proportion = minimum_proportion,
-			.abundance = !!.abundance
+			.abundance = !!.abundance,
+			design = design
 		)
 
 	.data[rowData(.data)$.abundant,]
@@ -2818,14 +2822,14 @@ setMethod("describe_transcript", "RangedSummarizedExperiment", .describe_transcr
 #' @importFrom SummarizedExperiment as.data.frame
 .resolve_complete_confounders_of_non_interest <- function(se, ...){
 
-  colData(se) = 
-    colData(se) |> 
-    as.data.frame() |> 
-    .resolve_complete_confounders_of_non_interest_df(...) |> 
+  colData(se) =
+    colData(se) |>
+    as.data.frame() |>
+    .resolve_complete_confounders_of_non_interest_df(...) |>
     DataFrame()
-  
+
   se
-    
+
 }
 
 #' resolve_complete_confounders_of_non_interest