gess_fisher() not working with msigdb in .h5 file

girke-lab / signatureSearch

R/Bioconductor package including the Gene Expression Signature Search (GESS), Function Enrichment Analysis (FEA) methods and supporting drug-target network construction for visualization

17 stars 4 forks source link

gess_fisher() not working with msigdb in .h5 file #11

Closed amackey closed 2 years ago

amackey commented 2 years ago

The gess_fisher function expects to find LINCS/CMAP-like annotations that wants to add to the result dataframe, e.g. calling sep_pcf() -- this causes the function to error.

brendangongol commented 2 years ago

Thank you for bringing this to my attention. I have modified the function to include an additional argument (addAnnotations). If you set addAnnotations to FALSE, gess_fisher() will not annotate the result dataframe with LINCS/CMAP-like annotations and the function should run to completion.

Regards, Brendan