NEWS

Changes for R-package epilab

Version 0.5-0 (March 25th, 2014)
  - Added functions for computing different standardized effect size metrics.
    - Cliff's Delta.
    - Camblor's AC. This is a new implementation fixing some previous errors in the lab's code.
    - Odds Ratio.
    - Odds Ratio for a given level of a big contingency table.
  - Added tests for the new functions.

Version 0.4-1 (March 18th, 2014)
  - Refactorization of FilterCommand execute() implementations, in order to make them work with
    the ANY signature.
  - Added some tests to see if the Filter hierarchy is working with GenomicMethylSet objects.

Version 0.4-0 (March 17th, 2014)
  - Added functions for the evaluation of overlap information between Illumin450k probes and genes.
    - getProbeGeneRelationship() for finding overlaps.
    - getGeneEntrezIds() for finding the set of genes represented by a set of probes.
    - getSymbolsFromEntrezIds() for extracting the gene names from their Entrez ID.

Version 0.3-0 (March 14th, 2014)
  - Added FilterCommand hierarchy for implementing chainable filtering mechanisms.
  - Added two simple filters:
    - A KOverA filter for removing bad samples according to their detection p-values.
    - A Var filter for implementing non-specific filtering.

Version 0.2-1 (March 3rd, 2014)
  - The distance to TSS calculation is now included in the NearestGene annotation command.

Version 0.2-0 (February 24th, 2014)
  - First version of package with some functionality.
  - It should be possible now to use the package for the annotation generation in most of our
    current 450k pipelines.
  - A hierarchy of Command objects is implemented for the annotation of GenomicRanges objects.
  - All commands are currently being tested.
  - Some setters are not implemented (low priority).