ActivePathways 1.1.0

Major Changes

ActivePathways 1.1.0

• Updated the filtering procedure of gene sets in the GMT file in cases where a custom gene background set is provided. Given a custom background gene set, the GMT gene sets are first modified to only include the genes of the background set, and second, the gene sets are filtered by gene set size. Gene sets including no genes of the background set are removed. This update will result in a more lenient multiple testing correction in analyses with custom background gene sets may cause different gene sets to be tested due to set size filters being applied after background filtering of gene sets.

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.