diff --git a/R/00-setup_data.R b/R/00-setup_data.R index 08ed602..a8e2f81 100644 --- a/R/00-setup_data.R +++ b/R/00-setup_data.R @@ -57,9 +57,6 @@ setup_data <- function(counts = NULL, pg_metadata = NULL, sample_metadata = NULL # Calculate the counts per sample new_data$counts_per_sample <- apply(counts, 2, sum) - # Calculate the coverage per pgRNA - new_data$coverage <- new_data$counts_per_sample/nrow(counts) - # Transform the data new_data$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)