Hi Rafael,
I found another infelicity that I think would be helped if were to attempt, at least to remap all of their phenotypes using text2term.
Note that this record:
gwascatmeta[gwascatmeta$STUDY.ACCESSION=="GCST90043950",]
PUBMEDID FIRST AUTHOR DATE JOURNAL LINK
79568 34737426 Jiang L 2021-11-04 Nat Genet www.ncbi.nlm.nih.gov/pubmed/34737426
STUDY
79568 A generalized linear mixed model association tool for biobank-scale data.
DISEASE.TRAIT
79568 Hypertensive chronic kidney disease (PheCode 401.22)
INITIAL SAMPLE SIZE REPLICATION SAMPLE SIZE
79568 365 European ancestry cases, 455,983 European ancestry controls
PLATFORM [SNPS PASSING QC] ASSOCIATION COUNT MAPPED_TRAIT MAPPED_TRAIT_URI
79568 NR [11842647] (imputed) 0 disease http://www.ebi.ac.uk/efo/EFO_0000408
STUDY.ACCESSION GENOTYPING TECHNOLOGY MAPPED_TRAIT_CURIE
79568 GCST90043950 Genome-wide genotyping array EFO:0000408
Is basically mapped to the very general "disease" term - not the obvious chronic kidney disease, or perhaps even there
is Hypertensive chronic kidney disease...
So putting this is in as a wish list - probably worth remapping all of the traits (note they have these PheCodes - I sent you a link) that seem to map to ICDxx - and we probably should be using that for Inovalon...
Hi Rafael, I found another infelicity that I think would be helped if were to attempt, at least to remap all of their phenotypes using text2term. Note that this record: gwascatmeta[gwascatmeta$STUDY.ACCESSION=="GCST90043950",] PUBMEDID FIRST AUTHOR DATE JOURNAL LINK 79568 34737426 Jiang L 2021-11-04 Nat Genet www.ncbi.nlm.nih.gov/pubmed/34737426 STUDY 79568 A generalized linear mixed model association tool for biobank-scale data. DISEASE.TRAIT 79568 Hypertensive chronic kidney disease (PheCode 401.22) INITIAL SAMPLE SIZE REPLICATION SAMPLE SIZE 79568 365 European ancestry cases, 455,983 European ancestry controls
PLATFORM [SNPS PASSING QC] ASSOCIATION COUNT MAPPED_TRAIT MAPPED_TRAIT_URI
79568 NR [11842647] (imputed) 0 disease http://www.ebi.ac.uk/efo/EFO_0000408
STUDY.ACCESSION GENOTYPING TECHNOLOGY MAPPED_TRAIT_CURIE
79568 GCST90043950 Genome-wide genotyping array EFO:0000408
Is basically mapped to the very general "disease" term - not the obvious chronic kidney disease, or perhaps even there is Hypertensive chronic kidney disease...
So putting this is in as a wish list - probably worth remapping all of the traits (note they have these PheCodes - I sent you a link) that seem to map to ICDxx - and we probably should be using that for Inovalon...