Merge branch 'cansavvy/datasetup' of https://github.com/FredHutch/gimap…

… into cansavvy/datasetup
FredHutch · Jan 31, 2024 · 655a7fb · 655a7fb
2 parents f79b448 + add7a3f
commit 655a7fb
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/R/00-setup_data.R b/R/00-setup_data.R
@@ -61,7 +61,7 @@ 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)