Fix normalization calculation

FredHutch · Jan 31, 2024 · add7a3f · add7a3f
1 parent 9bde86d
commit add7a3f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/R/00-setup_data.R b/R/00-setup_data.R
@@ -56,7 +56,7 @@ setup_data <- function(counts = NULL, pg_metadata = NULL, sample_metadata = NULL
   new_data$coverage <- new_data$counts_per_sample/nrow(counts)
 
   # Transform the data
-  new_data$transformed_data$count_norm <- -log10((counts + 1)/sum(counts))
+  new_data$transformed_data$count_norm <- apply(counts, 2, function(x) -log10((x+1)/sum(x)))
   new_data$transformed_data$cpm <- apply(counts, 2, function(x) (x/new_data$counts_per_sample)*1e6)
   new_data$transformed_data$log2_cpm <- log2(new_data$cpm +1)