issue with get_normalized_count_table.R

[Malabady]

Hi,
I am having an issue with the R script `get_normalized_count_table.R'. Basically, when I run this script I get the following error:

Error in `[.data.frame`(complete_table, , lapply(.SD, sum), by = complete_table$Row.names) :
  unused argument (by = complete_table$Row.names)
Calls: [
Execution halted

I started debugging the script by running it step by step and found the error at the following part of the code:

# reducing stuff down to avoid duplicates
complete_table <- complete_table[, lapply(.SD, sum), by=complete_table$Row.names]

I have tried many modifications of this line of the code but none worked.

Any help will be much appreciated.

Best,