| Title: | Tidy, Integrated Gene Annotation |
| Version: | 0.1.1 |
| Maintainer: | MD. Arshad <arshad10867c@gmail.com> |
| Description: | A framework for intuitive, multi-source gene and protein annotation, with a focus on integrating functional genomics with disease and drug data for translational insights. Methods used include g:Profiler (Raudvere et al. (2019) <doi:10.1093/nar/gkz369>), biomaRt (Durinck et al. (2009) <doi:10.1038/nprot.2009.97>), and the Open Targets Platform (Koscielny et al. (2017) <doi:10.1093/nar/gkw1055>). |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.3 |
| VignetteBuilder: | knitr |
| Imports: | dplyr, gprofiler2, httr, jsonlite, purrr, tidyr, ggplot2, biomaRt, tibble, magrittr, later (≥ 1.3.1), testthat (≥ 3.0.0), knitr (≥ 1.50), rmarkdown |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2026-01-22 10:07:55 UTC; sulky |
| Author: | MD. Arshad [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2026-01-27 08:40:19 UTC |
Pipe operator
Description
See magrittr::%>% for details.
Value
The result of the right-hand side function.
Add disease association data
Description
Augments an annotaR object with disease association data from the OpenTargets platform.
Usage
add_disease_links(annotaR_object, score_threshold = 0.5)
Arguments
annotaR_object |
A tibble, typically from |
score_threshold |
Minimum association score (from 0 to 1) to include. Defaults to 0.5. |
Value
A new tibble with the original data joined with disease association columns (disease_name, association_score).
Examples
annotaR(c("TP53", "EGFR")) %>%
add_disease_links(score_threshold = 0.8)
Add known drug association data
Description
Augments an annotaR object with known drug/compound data from the OpenTargets platform. This includes the drug name, type, mechanism of action, and clinical trial phase.
Usage
add_drug_links(annotaR_object)
Arguments
annotaR_object |
A tibble, typically from |
Value
A new tibble with the original data joined with drug association columns (e.g., drug_name, drug_type, mechanism_of_action, phase).
Examples
annotaR(c("EGFR", "BRAF")) %>%
add_drug_links()
Add GO functional enrichment data
Description
Augments an annotaR object with functional enrichment data from g:Profiler. It performs a Gene Ontology (GO) analysis on the gene list and joins the results.
Usage
add_go_terms(annotaR_object, organism = "hsapiens", sources = c("GO:BP"), ...)
Arguments
annotaR_object |
A tibble, typically the output of |
organism |
The organism name to use for the query (e.g., "hsapiens").
Passed to |
sources |
A vector of data sources to query. Defaults to GO Biological
Process. See |
... |
Additional parameters passed on to |
Value
A new tibble with the original 'gene' column joined with functional annotation columns (e.g., term_id, term_name, p_value, source).
Examples
annotaR(c("TP53", "EGFR")) %>%
add_go_terms()
Create an annotaR object
Description
Initializes the annotation pipeline by creating a tibble from a character vector of gene symbols. This is the entry point for a typical annotaR workflow.
Usage
annotaR(genes)
Arguments
genes |
A character vector of HGNC gene symbols (e.g., c("TP53", "BRCA1")). |
Value
A tibble with a single column 'gene', ready to be used in downstream annotation functions.
Examples
my_genes <- c("TP53", "EGFR", "BRCA1")
annotaR(my_genes)
Plot GO Enrichment Results as a Dot Plot
Description
Creates a publication-ready dot plot from the results of an
add_go_terms() call. The plot shows the top enriched terms, with dot
size representing the number of genes and color representing the p-value.
Usage
plot_enrichment_dotplot(
annotaR_object,
n_terms = 20,
title = "Top GO Enrichment Results"
)
Arguments
annotaR_object |
An object processed by |
n_terms |
The maximum number of top terms to display, ordered by p-value. Defaults to 20. |
title |
The title of the plot. |
Value
A ggplot object.
Examples
# Create a dummy annotaR object with enrichment data
annotated_data <- tibble::tibble(
gene = c("TP53", "TP53", "EGFR"),
term_name = c("Cell cycle", "Apoptosis", "Cell cycle"),
p_value = c(0.001, 0.005, 0.001),
source = "GO:BP",
intersection = "TP53,EGFR"
)
plot_enrichment_dotplot(annotated_data)