Week five | TumorComparer on Gene Subsets

This week I was calculating comparisons for 10 specified genesets. During the calculation, we detected some technical issues and exceptions which were not covered by package functions. With the help of my mentor, I have updated package functions to handle exceptions and missing values.

Work Progress

1. TumorComparer on Gene Subsets
   Status։ Done
   Issue: TumorComparer on Gene Subsets

2. Reproducibility of the results
   Status։ Done
   Issue: Testing Geneset Specific Function

3. Missing values and exceptions
   Status։ Done
   Issue: Geneset filtering issue

4. Missing values and exceptions
   Status։ Done
   Issue: Datatypes with zero values in precomputed comparisons

5. Missing values and exceptions
   Status։ Done
   Issue: Add Test that Triggers to Few Genes in Comparison

6. Missing values and exceptions
   Status։ Done
   Issue: Comparison function error with LIHC cancer type in TGF-Beta pathway

Conclusion

I have finished precalculation of comparisons for 10 genesets in 23 cancer types, updated package functions to handle missing and zero values. On top of that, I have updated the generalized comparison function to perform comparison for specified gene list.