NEWS

otargen 1.1.5 (2024-09-21)

chemblQuery(): This function queries the Open Targets GraphQL API to retrieve ChEMBL data for a specified gene and disease, including evidence from the ChEMBL datasource.
- clinvarQuery(): #' This function queries the Open Targets GraphQL API to retrieve ClinVar data for a specified gene and disease, including evidence from the NCBI datasource.
- knownDrugsQuery(): This function queries the Open Targets GraphQL API to retrieve known drugs data for a specified gene.
- mousePhenotypesQuery(): This function queries the Open Targets GraphQL API to retrieve mouse phenotypes data for a specified gene.
- compGenomicsQuery() This function queries the Open Targets GraphQL API to retrieve comparative genomics data for a specified gene.

Fixed several inconsistencies between parameters naming in the functions used in the examples article and the main function in the package.
- Streamline the examples description to be short and organized.
- Added additional plotting case for example 7 for the additional parameters that has been added in the current version to the plot_l2g function.

Fixed and issue with the plot_l2g() function for the cases when the disease parameter were not selected. The previous function were plotting only top disease for one gene. The function now updated with two more parameters to expand the plot_l2g() functionality for plotting disease agnostic scenario. These two parameters are:
- top_n_disease (default: 1): Determines the number of top diseases to plot for each gene, ranked by L2G score. Increase this value to include more diseases in the analysis. Use in conjunction with being disease-agnostic to dynamically select the top diseases for each gene.

l2g_cutoff (default: 0.5): Sets the minimum L2G score threshold for diseases to be considered in the plot. Increasing this value can help reduce plot clutter by focusing on higher-confidence associations.

Fixed an issue in the variantInfo function where the wrong variable (result) was being referenced, leading to an 'object not found' error. Modified variantInfo() to correctly process the API response data. Additionally, added checks to ensure that the results are not NULL before processing, which improves the function's robustness and error handling.

Improved the test plot_l2g.R test case to provide better error handling and diagnostic information. The test now uses a tryCatch block to gracefully handle errors and explicitly fail with a clear message, enhancing the reliability and maintainability of the test suite.

Fixed the issue with genesForVariant() on giving an error when using rsId variants.

Updated all functions to include connection timeout checks. Added try-catch blocks to handle timeouts during API requests gracefully, ensuring that the functions provide informative error messages and fail safely in case of network or connection issues.