get_counts fixed

seoanezonjic · Jan 23, 2024 · 667ac1f · 667ac1f
1 parent d5baa17
commit 667ac1f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/R/main_degenes_Hunter.R b/R/main_degenes_Hunter.R
@@ -439,7 +439,7 @@ filter_by_variance <- function(count_matrix, q_filter, target){
                                   colData = target,
                                   design = stats::formula("~ treat"))
   dds <- DESeq2::DESeq(dds)
-  normalized_counts <-DESeq2::counts(dds, normalized=TRUE)
+  normalized_counts <- DESeq2::counts(dds, normalized=TRUE)
   variances <- matrixStats::rowVars(normalized_counts)
   threshold <- stats::quantile(variances, q_filter)
   fil_count_mtrx <- count_matrix[variances >= threshold,]