How to calculate co-dependencies locally?

Q&A
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Hi there,

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.

  1. 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?

  1. 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?
2

Yes, the script is computing the Pearson correlation coefficient.

And also, yes, if you want to compute co-dependencies, you would provide the same file twice.

You could also use it to compute correlations between two different datasets such as gene effect and expression, which is why it takes two files. However, if co-dependency is what you want, you’d correlate all entries in Achilles_gene_effect.csv with all entries in Achilles_gene_effect.csv

Thanks,
Phil