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intermine / InterMineR

R package for InterMine
GNU Lesser General Public License v2.1
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convertToGeneAnswers should accept list names #61

Open yochannah opened 5 years ago

yochannah commented 5 years ago

convertToGeneAnswers constitutes a wrapper function for converting the results of the doEnrichment function to a GeneAnswers-class object.

To run this function, one must pass a data.frame containing the gene identifiers that were enriched on as the geneInput argument.

Given that enrichment can be run using either a list of ids or an InterMine list name, it would make sense if convertToGeneAnswers would accept a list name for geneInput as well - otherwise we have to run a query to fetch the list contents client side, even though we didn't need to do this for the enrichment in the previous step.

yochannah commented 5 years ago

... The code also seems to run a new LOOKUP query for every single value in the list, which can take ages.

For large queries it is probably much simpler to pass in the list name and probably much faster