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Package: HPOExplorer | ||
Title: Analysis and Visualisation of the Human Phenotype Ontology | ||
Version: 0.99.12 | ||
Version: 1.0.0 | ||
Authors@R: | ||
c( | ||
person(given = "Brian", | ||
|
@@ -18,25 +18,21 @@ Authors@R: | |
role = c("aut"), | ||
email = "[email protected]", | ||
comment = c(ORCID = "0000-0002-6807-3180"))) | ||
Description: HPOExplorer contains useful functions for working with | ||
the Human Phenotype Ontology (HPO). | ||
It allows you to create interactive phenotype network plots, | ||
which can be useful for making web applications. | ||
It also has functions for finding ontology level | ||
(n generations of terms below the selected term), | ||
and getting term definitions from HPO API. | ||
Description: Import, annotate and visualise the 18k+ hierarchically structured | ||
clinical phenotypes across the Human Phenotype Ontology. | ||
License: GPL-3 | ||
URL: https://github.com/neurogenomics/HPOExplorer | ||
BugReports: https://github.com/neurogenomics/HPOExplorer/issues | ||
Encoding: UTF-8 | ||
Roxygen: list(markdown = TRUE) | ||
RoxygenNote: 7.2.3 | ||
RoxygenNote: 7.3.0 | ||
Depends: | ||
R (>= 4.1.0) | ||
Imports: | ||
KGExplorer, | ||
simona, | ||
ggplot2, | ||
plotly, | ||
ontologyIndex, | ||
plotly, | ||
utils, | ||
stats, | ||
methods, | ||
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@@ -45,31 +41,27 @@ Imports: | |
tools, | ||
data.table, | ||
stringr, | ||
EnsDb.Hsapiens.v75, | ||
ensembldb, | ||
AnnotationFilter, | ||
GenomicRanges, | ||
AnnotationHub | ||
GenomicRanges | ||
Suggests: | ||
rmarkdown, | ||
knitr, | ||
devtools, | ||
BiocStyle, | ||
rworkflows, | ||
here, | ||
httr, | ||
jsonlite, | ||
testthat (>= 3.0.0), | ||
igraph, | ||
pals, | ||
Matrix, | ||
MASS, | ||
scales, | ||
htmlwidgets, | ||
R.utils, | ||
piggyback, | ||
patchwork, | ||
BiocParallel | ||
igraph, | ||
tidygraph | ||
Remotes: | ||
github::neurogenomics/KGExplorer | ||
VignetteBuilder: knitr | ||
biocViews: | ||
Genetics, Preprocessing, GeneTarget, SystemsBiology, | ||
|
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#' @title Main functions | ||
#' | ||
#' @description | ||
#' Main functions. | ||
#' @param phenos A data.table containing HPO IDs and other metadata. | ||
#' @param hpo Human Phenotype Ontology object, | ||
#' loaded from \link[KGExplorer]{get_ontology}. | ||
#' @param add_ont_lvl_absolute Add the absolute ontology level of each HPO term. | ||
#' See \link[KGExplorer]{get_ontology_levels} for more details. | ||
#' @param add_ont_lvl_relative Add the relative ontology level of each HPO term. | ||
#' See \link[KGExplorer]{get_ontology_levels} for more details. | ||
#' @param add_description Whether to get the phenotype descriptions as | ||
#' well (slower). | ||
#' @param add_info_content Add information content column for each phenotype. | ||
#' @param add_disease_data Add all disease metadata columns. | ||
#' This will expand the data using \code{allow.cartesian=TRUE}. | ||
#' @param add_ndiseases Add the number of diseases per phenotype. | ||
#' @param add_pheno_frequencies Add the frequency of each phenotype in | ||
#' each disease. | ||
#' @param add_tiers Add severity Tiers column using | ||
#' \link[HPOExplorer]{add_tier}. | ||
#' @param add_severities Add severity column using | ||
#' \link[HPOExplorer]{add_severity}. | ||
#' @param add_hoverboxes Add hoverdata with | ||
#' \link[KGExplorer]{add_hoverboxes}. | ||
#' @param add_onsets Add age of onset columns using | ||
#' \link[HPOExplorer]{add_onset}. | ||
#' @param add_deaths Add age of death columns using | ||
#' \link[HPOExplorer]{add_death}. | ||
#' @param columns A named vector of columns in \code{phenos} | ||
#' to add to the hoverdata via \link[KGExplorer]{add_hoverboxes}. | ||
#' @param add_disease_definitions Add disease definitions. | ||
#' @param include_mondo Add \href{https://mondo.monarchinitiative.org/}{MONDO} | ||
#' IDs, names, and definitions to each disease. | ||
#' @param interactive Make the plot interactive. | ||
#' @family main | ||
#' @returns Data. | ||
#' @import data.table | ||
#' @import KGExplorer | ||
#' @name main | ||
NULL | ||
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#' @title Get functions | ||
#' | ||
#' @description | ||
#' Functions to get data objects and extract elements. | ||
#' @param term One or more ontology IDs. | ||
#' @family get_ | ||
#' @param force_new Force a new download or creation of a data resource. | ||
#' @param lvl How many levels deep into the ontology to get ancestors from. | ||
#' For example: | ||
#' \itemize{ | ||
#' \item{1: }{"All"} | ||
#' \item{2: }{"Phenotypic abnormality"} | ||
#' \item{3: }{"Abnormality of the nervous system"} | ||
#' \item{4: }{"Abnormality of nervous system physiology"} | ||
#' \item{5: }{"Neurodevelopmental abnormality" or "Behavioral abnormality"} | ||
#' } | ||
#' @inheritParams main | ||
#' @inheritParams make_ | ||
#' @returns Data. | ||
#' @name get_ | ||
NULL | ||
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#' @title Add functions | ||
#' | ||
#' @description | ||
#' Functions to add metadata to data.table objects. | ||
#' @family add_ | ||
#' @param agg_by Column to aggregate metadata by. | ||
#' @param add_definitions Add disease definitions using \link{add_mondo}. | ||
#' @inheritParams main | ||
#' @inheritParams make_ | ||
#' @inheritParams get_ | ||
#' @inheritParams data.table::merge.data.table | ||
#' @returns Annotated data. | ||
#' @name add_ | ||
NULL | ||
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#' @title Filter functions | ||
#' | ||
#' @description | ||
#' Functions to filter data.table objects. | ||
#' @family filter_ | ||
#' @inheritParams main | ||
#' @returns Filtered data. | ||
#' @name filter_ | ||
NULL | ||
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#' @title Map functions | ||
#' | ||
#' @description | ||
#' Functions to map IDs. | ||
#' @family map_ | ||
#' @inheritParams main | ||
#' @inheritParams KGExplorer::map_ontology_terms | ||
#' @returns Mapped data. | ||
#' @name map_ | ||
NULL | ||
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#' @title Make functions | ||
#' | ||
#' @description | ||
#' Functions to make complex R objects. | ||
#' @param as R object class to return output as. | ||
#' @param phenotype_to_genes Output of | ||
#' \link{load_phenotype_to_genes} mapping phenotypes | ||
#' to gene annotations. | ||
#' @param ancestor The ancestor to get all descendants of. If \code{NULL}, | ||
#' returns the entirely ontology. | ||
#' @family make_ | ||
#' @inheritParams main | ||
#' @returns R object. | ||
#' @name make_ | ||
NULL |
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