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kkdey / GSSG

Gene Set + S2G strategy annotations analyzed for disease architecture
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How to calculate the Escore and pEscore？ #11

Closed bitcometz closed 3 years ago

bitcometz commented 3 years ago

hello， In your supplementary files from your sc-linker paper, there are escores for the cell types: image

Could you tell me how these escores were calculated ？ Is it obtained from this R: https://github.com/kkdey/GSSG/blob/master/code/ldsc/ldsc_postprocess_enrichment.R

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kkdey commented 3 years ago

@bitcometz Yes you can get the enrichment values for the annotation (Gene score x S2G) using this code from the sc-linker heritability analysis output, and do the same for the respective (All genes x S2G), and take the difference. Thats the E-score. The E-score if < 0 is taken as 0, as then it means the gene score is not informative over all genes.