Hi,
I am trying to recreate the DepMap dependency tag using your RNAi and CRISPR data which is described as: ‘a cell line is considered dependent if it has a probability of dependency greater than 0.5’
However, when using this simple function as described [1], the number of cell lines labelled as dependent is similar but not equal to what is displayed online.
Is there further filtering done to the dependence cell line value?
Thankyou,
Jude
[1] (is_dependent ← function(score, threshold = -0.5) {
if (is.na(score)) {
return(FALSE)
} else {
return(score < threshold)
}
})
In your code, I see you have the parameter named score.
Are you perhaps not thresholding “probability of dependency” (which is from CRISPRGeneDependency ) and and instead thresholding “Gene effect score” (which is from CRISPRGeneEffect.csv.csv )
For binarizing lines into dependent-or-not-dependent, you’ll want to make sure you’re using the values from CRISPRGeneDependency.csv
Thanks,
Phil
You are correct, thank you. In the end I found that that doing this on dependency scores achieved similar but not the exact same value as on the portal; however, I found an API request in this forum that internally scrapes the page and provides this information anyway!
