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NEWS.md

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ActivePathways 2.0.5

  • Fixed a minor bug when exporting results from the ActivePathways() output as a data.table into a csv file. Thre bug occurred when all results unfiltered by statistical significance values were exported, resulting in NULL values in gene overlap columns of resulting tables. These NULL entries are now first converted to an empty string inside the export_as_CSV() function.

ActivePathways 2.0.4

  • Minor update to ensure the 'scores' and 'scores_direction' matrices have the same number of rows, and that the gene row names in 'scores' are in the same order as 'scores_direction'. The method now reports an error and terminates if two matrices are misaligned.

ActivePathways 2.0.3

  • Minor updates in documentation and code examples.

ActivePathways 2.0.2

  • Separated the directional P-value merging methods into separate functions. 'Fisher_directional', 'DPM', 'Stouffer_directional', and 'Strube_directional' methods perform directional integration. The 'scores_direction' and 'constraints_vector' parameters must be provided.

ActivePathways 2.0.1

  • Changed how very small P-values are processed before P-value merging. P-values of '0' or anything less than '1e-300' are converted to '1e-300'.

ActivePathways 2.0.0

  • Incorporated 'scores_direction' and 'constraints_vector' parameters to ActivePathways() and merge_p_values() to account for the direction between datasets when performing p-value merging.
  • Added the 'Stouffer' and 'Strube' p-value merging methods as alternatives to 'Fisher' and "Brown', respectively.
  • Changed the naming convention of parameters and objects, substituting a period '.' for an underscore '_'.

ActivePathways 1.1.1

  • Added an option for the colours specified in the "custom_colors" parameter to be provided in any order, as long as the vector "names()" match the column names of the "scores" matrix.
  • Fixed an error where the "combined" contribution label was absent from the legend.pdf ActivePathways output file.

ActivePathways 1.1.0

  • Updated the filtering procedure of gene sets in the GMT file when a custom gene background is provided. Given a background gene list, the GMT gene sets are first modified to only include the genes of the background list, and second, the gene sets are filtered by gene set size. Gene sets lacking any genes from the background list are removed. This update will result in a more lenient multiple testing correction in analyses with a custom background gene list.

ActivePathways 1.0.4

  • Added three new parameters to ActivePathways and prepareCystoscape functions. These include "color_palette", "custom_colors" and "color_integrated_only" to provide more options for node coloring in Cytoscape.

ActivePathways 1.0.3

  • Removed dependency used for testing for CRAN compliance.

ActivePathways 1.0.2

  • Renamed package to ActivePathways from activePathways for consistency with function and publication
  • Added new function export_as_CSV(res, file_name) to save data in spreadsheet-friendly formats
  • Updated README-file with an actionable step-by-step tutorial
  • Changed logic of creating files for Enrichment Map: the user can provide the parameter "cytoscape.file.tag" for creating the required files. If the parameter is NA (default), no files are created. No directories are created.
  • Removed the parameter "return.all" as it was redundant with the parameter "significance".
  • Removed the parameter "reanalyze" to simplify the package and leave the structuring of results up to the user.
  • Removed the dependency on the R package metap. As a result, only Fisher's and Brown's p-value merging options are available.
  • Updated the vignette that now describes the ActivePathways package as well as the following steps of visualising results as enrichment maps in Cytoscape.