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Fix moonlight z-score and updated datasets accordingly#169

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fix168_moonlight_fea_zscore
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Fix moonlight z-score and updated datasets accordingly#169
AlessiaCampo wants to merge 1 commit into
develfrom
fix168_moonlight_fea_zscore

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The present PR contains changes to fix the Moonlight Z-score calculation within the FEA() function. The fix include the replacement of the experimental Exp.Log.Ratio taken from the DiseaseList dataset with the experimental logFC taken from the input DEGs or DAPs matrix.
Since the FEA function now implements two different statistical method to perform the analysis (namely Fisher test ora-based method and fgsea method), the moonlight z-score calculation has been updated to make sense in both cases:

  • For the ora-based method the Moonlight Z-score is computed over all the genes that overlap the input gene list and the BP gene set (as it was done in the previous implementations)
  • For the fgsea method, the Moonlight Z-score calculation is computed over all the genes that are part of the leadingEdge list, which is the list of genes found to be enriched in a given BP and are predicted to be the ones contributing more to the enrichment of the BP.

The difference between the two scores is the population of genes used to compute the z-score: in the ora-based method we assume that the input data matrix has been filtered to contain only the significant DEGs, while the fgsea method consider all the genes in input for the enrichment calculations. For this reason, we only take into account the leading edge genes (the most relevant ones) for the score calculation.

Linked to the change of the moonlight z-score, additional updates were made on the datasets stored in data/:

  • dataFEA containing the new scores
  • dataURA which uses FEA internally
  • dataPRA which uses dataURA as input

To make run tests and examples smoothly, toghether with the new Z-scores, the dataGRN was updated to include more TFs so that the other downstream analysis and function using these data (i.e. URA, FEA, PRA, TFinfluence) would work with no issues.

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