R-outbreak-info
R-outbreak-info copied to clipboard
Genomics API: getPrevalence() does not accept deletions
Submitted by user: I noticed a pretty significant limitation in the getPrevalence() function: the function does not accept deletions. This is the error message I’ve seen (using a deletion found in omicron, which is also the example from the outbreak.info site which shows how to format deletion mutation names):
In getGenomicData(query_url = "prevalence-by-location", pangolin_lineage = pangolin_lineage, : Mutations should be specified in the format gene:mutation, like "S:E484K". The following mutations are not in the specified format: S:DEL69/70