Merge pull request #20 from FredHutch/patch_cpm_calcs

fix cpm calculations
FredHutch · Mar 22, 2024 · 6027dad · 6027dad
2 parents 1e7217e + 6467636
commit 6027dad
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/R/00-setup_data.R b/R/00-setup_data.R
@@ -59,8 +59,8 @@ setup_data <- function(counts = NULL, pg_metadata = NULL, sample_metadata = NULL
 
   # Transform the data
   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)
+  new_data$transformed_data$cpm <- apply(counts, 2, function(x) (x/sum(x))*1e6)
+  new_data$transformed_data$log2_cpm <- log2(new_data$transformed_data$cpm +1)
 
   return(new_data)
 }