ActivePathways 1.0.2

Major Changes

• 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.