Annotate each HPO with modifier terms, including (but not limited to) progression and severity ratings. In order of increasing severity:
HP:0012825 "Mild" (Severity_score=4)
HP:0012827 "Borderline" (Severity_score=3)
HP:0012828 "Severe" (Severity_score=2)
HP:0012829"Profound" (Severity_score=1)
add_severity(
phenos,
hpo = get_hpo(),
all.x = TRUE,
allow.cartesian = FALSE,
severity_threshold = NULL,
verbose = TRUE
)dataframe of phenotypes and values / parameters.
Human Phenotype Ontology object, loaded from ontologyIndex.
logical; if TRUE, then extra rows will be added to the
output, one for each row in x that has no matching row in y.
These rows will have 'NA's in those columns that are usually filled with values
from y. The default is FALSE, so that only rows with data from both
x and y are included in the output.
See allow.cartesian in [.data.table.
Only keep phenotypes with a mean
severity score (averaged across multiple associated diseases) below the
set threshold. The severity score ranges from 1-4 where 1 is the MOST severe.
Include NA if you wish to retain phenotypes that
do not have any severity score.
Print messages.
phenos data.table with extra columns
phenos <- example_phenos()
#> ℹ All local files already up-to-date!
phenos2 <- add_severity(phenos = phenos)
#> Annotating phenos with modifiers
#> Annotating phenos with Disease
#> Reading cached RDS file: phenotype.hpoa
#> + Version: v2023-10-09