Do we consider the run_comparison function as a gene centered?

[hakobyansiras]

To specify some details about the requirements of the dataset input file I would like to know if we consider the run_comparison function to work only for gene based comparisons.

[cannin]

Not sure if I understand. run_comparison was there before the summer and it should continue working as it was before. As seen from our publication, it worked on gene lists like the most variable genes or pathway gene lists. For now, we have only tested/used it on entries with HGNC gene symbols. But as long as there are similarly-named entries present for both tumor and cell lines in a numeric vector representation it should work.

[hakobyansiras]

I am writing documentation for the new comparison function (run_comparison_config_list). As it is also capable to run comparison for specified gene list I am wondering if I should write that input data entries should be the genes with HGNC names or to change the "gene_list" argument name to something general.

[cannin]

I see. Keep it as gene_list. For most cases, this will make sense. More advanced users may see this message or contact us.