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Option to assign single enrichment score instead of scores per bins #48

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abearab opened this issue Nov 30, 2023 · 1 comment
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@abearab
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abearab commented Nov 30, 2023

It will be very useful to have the option to get single enrichment score for up / down regulated genesets. I'm not sure if this is already implemented, plz let me know if I'm missing it.

Here I have function called pvmat2bio_signal which aims to identify up / down regulated genesets (mostly enriched in top right or top left bins). However, it's useful to have a single enrichment score instead of a vector of scores for bins. Long time ago when I discussed something like this with @hanig, he pointed to this figure in original iPAGE paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900319/figure/F5/.

I'll be happy to share a PR but I'm not sure how to convert a vector of score to single value. For instance, in this analysis how should a pathway with high score in three left bins be scored with a single number?

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@hanig
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hanig commented Nov 30, 2023

The best way to convert an enrichment/depletion map to a single score is calculating the Spearman correlation between enrichment scores and bin numbers from left to right. So, in the example above from @abearab, the MYC targets will have a very negative Spearman correlation, and NFKB will have a positive one. This basically implies a monotonically increasing or decreasing pattern.

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