You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The text was updated successfully, but these errors were encountered:
Recent use of the getPrevalence function shows that searching S:DEL69/70 is possible, ONLY IF an accompanying lineage is searched for as well, this issue is recently raised in #104 .
Interestingly the mutation is presented differently in the getMutationDetails() Function:
> getMutationDetails(mutations=c("S:DEL69/70"))
Retrieving data...
mutation is_synonymous codon_num ref_codon absolute_coords gene pos is_frameshift deletion_codon_coords type
1 S:DEL69/70 False 68 CATGTC 21765:21770 S 21765 False S:DEL68.2/70.1 deletion
Warning message:
In getGenomicData(query_url = "mutation-details", mutations = mutations) :
Mutations should be specified in the format gene:mutation, like "S:E484K". The following mutations are not in the specified format: S:DEL69/70
This shows that it is able to recognise the DEL69/70 mutation, but perhaps the warning message should be changed.
TKMarkCheng
added a commit
to TKMarkCheng/R-outbreak-info
that referenced
this issue
Mar 5, 2023
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):
The text was updated successfully, but these errors were encountered: