NEWS.md
make_phenos_dataframe
.hpo_api
as the HPO API was deprecated in the 2.0.0 Release (https://hpo.jax.org/data/api).ontologyIndex
to simona
, which seems to be better written and has extensive analysis functions.KnowledgeNets
get_prevalence_orphanet
get_prevalence_oard
map_upheno
map_upheno_data
map_upheno_plots
map_upheno_heatmap
map_upheno_rainplot
map_upheno_scatterplot
get_monarch
get_monarch_models
convert_hpo
add_medgen
add_omop
add_prevalence
add_prevalence_report
dt_to_matrix
add_mondo
map_mondo
get_hpo
gpt_annot_*
get_hpo
: already built in to ontologyIndex
objects.load_phenotypes_to_genes
: new attribute.get_version
clear_cache
make_ontology
internal function.create_node_data
–> make_node_data
get_gencc
gpt_annot_read
gpt_annot_check
gpt_annot_codify
gpt_annot_plot
get_hpo
ontologyIndex::get_OBO
.load_phenotype_to_genes
:
test-get_ont_lvls
example_phenos
load_phenotype_to_genes
hpo
object to “2023-06-17” release.load_phenotype_to_genes
get_gene_lengths
keep_seqnames=NULL
.add_genes
phenos_to_granges
code.extract_tags = "everything"
.xref
to get HPO ID mappings with other databases (MESH, SNOMED, UMLS).piggyback
to reduce package size.get_mondo
xref
to get HPO ID mappings with other databases (DOID, MESH, ICD9, GARD, EFO, SCTID, NCIT UMLS, Orphanet).get_data
piggyback
data.hpo_meta
hpo
tags: hpo$def
, hpo$xref
, etc.example_phenos
:
hpo
object:
ontologyIndex
) with an updated one from 2023.HPOExplorer
that may have relied on hpo
to be generated.fix_hpo_ids
hpo_tiers
:
map_phenotypes
output.hpo_tiers
csv to inst/extdata.get_hpo_id
function in favor of get_hpo_id_direct
which is more reliable and comprehensive.get_ont_lvls
:
get_max_ont_lvl
make_network_object
:
list_columns
so that ontLvl_relative
gets added to network obj.list_columns
extra_cols
get_hpo()
wesanderson
from deps.make_hoverbox
get_disease_description_dataframe
hpo_tiers
data from Momoko’s thesis.make_phenos_dataframe
far more efficient.adjacency_matrix
:
ontologyIndex::get_term_descendancy_matrix
load_phenotype_to_genes
:
phenos_to_granges
add_onset
add_tier
map_phenotypes
get_gene_lists
get_gene_lengths
list_onsets
NEWS.md
file to track changes to the package.rworkflows
make_network_plot
: make interactive with plotly
make_hoverboxes
make_phenos_dataframe
verbose
arg throughout.load_phenotype_to_genes
as_ascii