News

activePathways 1.0.1

Major Changes

• Rename to activePathways

activeDriverPW 1.0.0

Major Changes

• Add a geneset.filter option to activeDriverPW to filter the GMT by geneset size
• Add vignettes
• Export merge_p_values method

activeDriverPW 0.0.0.9002

Major changes

• Rename to activeDriverPW

mpea 0.0.0.9001

Major Changes

• Change column contribution method. Column contribution is now reported as the log-fold-change when the column is excluded. ie, -log10(p_val_with_column / p_val_without_column)

Minor Changes

• No longer raises an error if no significant terms are found and return.all is false. Instead returns an empty data.table and issues a warning.
• Issue a warning if genes are filtered out for not being found in the background
• Change default p-value adjustment method to "holm"
• If return.all==FALSE, calculates columnContribution only for terms that will returned. Speeds up runtime by roughly a factor of 2
• Add "none" option to p-value adjustment methods
• New implementation of orderedHypergeometric function which is several times faster.

Bug fixes

• Fix Brown's method when all p-values in a column are the same
• Fix in orderedHypergeometric which added an extra NA to the complement, leading to small errors in the calculated p-value
• Fixed another bug in orderedHypergeometric which added an extra NA to the complement in some cases, leading to small errors in the calculated p-value

mpea 0.0.0.9000

• Initial Build

• Added a NEWS.md file to track changes to the package.

Reference manual