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DiseaseOntology / DO.utils

R package for improvement and analysis of the Human Disease Ontology (DO), including semi-automated use assessment from published literature.
https://diseaseontology.github.io/DO.utils/
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Expand accepted inputs to inventory_omim() #20

Open allenbaron opened 7 months ago

allenbaron commented 7 months ago

Need to expand the accepted inputs to inventory_omim() to include data.frames without omim_tbl class.

Probably easiest to add an initial test to identify input that is a data.frame versus a character vector (i.e. filepath) and then check for omim_tbl class.

For non-omim_tbl data.frames, there should probably be another argument that allows specifying the name of the column with the OMIM xrefs in it. This would avoid the need to change the column's name to omim before running the inventory. _Maybe this should be expanded to tables with omim_tbl class as well, in case the name is changed?_

allenbaron commented 6 months ago

Also would be helpful to be able to process tables from OMIM gene pages, like https://www.omim.org/entry/114205?search=CACNA1C&highlight=cacna1c.

Doesn't process header correctly or add OMIM column as expected.