Dear David,
I am running some templates from biokitr and found out an issue with mouse <-> human orthologs. My dataset is mouse but not all of genes were being annotated with the human ortholog, despite they being well known (e.g. Cxcl11 = CXCL11). I went to the code, and it uses ribiosAnnotation function:
orths <- data.table(getHumanOrthologs(organism, useRibios = TRUE))
This function can have 2 routes if we have ribiosAnnotation credentials (which I have now in my home as specified)
However, the function fails because of the following error:
Error in rjson::fromJSON(file = file) : not all data was parsed (570 chars were parsed out of a total of 950 chars)
Have you encounter this before?
I have tested with R4.1.2 and R4.2.0 (sHPC).
Thanks, Martha
Dear David,
I am running some templates from biokitr and found out an issue with mouse <-> human orthologs. My dataset is mouse but not all of genes were being annotated with the human ortholog, despite they being well known (e.g. Cxcl11 = CXCL11). I went to the code, and it uses ribiosAnnotation function:
orths <- data.table(getHumanOrthologs(organism, useRibios = TRUE))This function can have 2 routes if we have ribiosAnnotation credentials (which I have now in my home as specified)
However, the function fails because of the following error:
Error in rjson::fromJSON(file = file) : not all data was parsed (570 chars were parsed out of a total of 950 chars)Have you encounter this before?
I have tested with R4.1.2 and R4.2.0 (sHPC).
Thanks, Martha