I’m trying to calculate co-dependencies locally with python. I noted that a post has already discussed it but, I still have some questions.
- I noted that pmontgom posted his python code at Script based on code from the DepMap portal code to compute the top N pearson correlations and write to a CSV file · GitHub, and suggested us run it with
python scripts/correlation_from_csv.py Achilles_gene_effect.csv Achilles_gene_effect.csv --limit 10 out.csv
Do the two input csv files have to be the same? That is, this means that if I want to calculate gene co-dependencies based on CRISPR/Cas9 data, I just need to replace both csv files with the CRISPR_gene_effect.csv downloaded from the Depmap portal?
- Is the method used to calculate co-dependencies the Pearson correlation coefficient? That is, if I need to calculate the partners of gene A, I just need an input file (CRISPR_gene_effect.csv) and then calculate the correlation coefficients of gene A with all other genes?