CHANGES IN VERSION 1.0
----------------------

PKG FEATURES

  o chipenrich performs gene set enrichment tests on peaks called from
    a ChIP-seq experiment

  o chipenrich empirically corrects for confounding factors such as 
    the length of genes and mappability of sequence surrounding genes

  o Use multiple definitions of a gene "locus" when testing for enrichment, 
    or provide your own definition

  o Test for enrichment using chipenrich or Fisher's exact test (should only
    be used for datasets where peaks are close to TSSs, see docs)

  o Test multiple sets of genesets (Gene Ontology, KEGG, Biocarta, OMIM, etc.)

  o Multiple plots to describe binding distance and likelihood of a peak
    as a function of gene length

  o Support for human (hg19), mouse (mm9), and rat (rn4) genomes

  o Many conveniences such as seeing which peaks were assigned to genes, 
    their position relative to those genes and their TSS, etc.

  o See how many peaks were assigned to each gene along with the length and
    mappability of the gene


CHANGES IN VERSION 0.99.2
-------------------------

USER-VISIBLE CHANGES

  o Updated examples for various functions to be runnable (removed donttest)
  o Updated DESCRIPTION to use Imports: rather than Depends:
  o Updated license to GPL-3
  o Updated NEWS file for bioconductor guidelines

BUG FIXES

  o Added a correction for the case where a small gene set has a peak in 
    every gene. This has the result of making a very few number of tests
    slightly conservative, at the benefit of actually being able to return
    a p-value for them. 

CHANGES IN VERSION 0.99.1
-------------------------

USER-VISIBLE CHANGES

  o Minor updates to documentation for Bioconductor

CHANGES IN VERSION 0.99.0
-------------------------

NEW FEATURES

  o Initial submission to Bioconductor

CHANGES IN VERSION 0.9.6
------------------------

NEW FEATURES

  o Added peaks per gene as a returned object / output file

CHANGES IN VERSION 0.9.5
------------------------

BUG FIXES

  o Update to handle bioconductor/IRange's new "functionality" for distanceToNearest and distance

USER-VISIBLE CHANGES

  o Changed sorting of results to put enriched terms first (sorted by p-value), then depleted (also sorted by p-value)

CHANGES IN VERSION 0.9.4
------------------------

USER-VISIBLE CHANGES

  o Minor changes to vignette and documentation

CHANGES IN VERSION 0.9.3
------------------------

NEW FEATURES

  o Addition of rat genome

BUG FIXES

  o chipenrich() will correctly open both .bed and .bed.gz files now

CHANGES IN VERSION 0.9.2
------------------------

NEW FEATURES

  o Added ability for user to input their own locus definition file (pass the full path to a file as the locusdef argument)
  o Added a data frame to the results object that gives the arguments/values passed to chipenrich, also written to file *_opts.tab
  o For FET and chipenrich methods, the outcome variable can be recoded to be >= 1 peak, 2 peaks, 3 peaks, etc. using the num_peak_threshold parameter
  o Added a parameter to set the maximum size of gene set that should be tested (defaults to 2000)

USER-VISIBLE CHANGES

  o Previously only peak midpoints were given in the peak --> gene assignments file, now the original peak start/ends are also given
  o Updated help/man with new parameters and more information about the results 

BUG FIXES

  o Fixed an issue where status in results was not enriched if the odds ratio was infinite, and depleted if the odds ratio was exactly zero

CHANGES IN VERSION 0.9.1
------------------------

NEW FEATURES

  o Added a QC plot for expected # of peaks and actual # of peaks vs. gene locus length. This will be automatically created if qc_plots is TRUE, or the plots can be created using the plot_expected_peaks function. 
  o Distance to TSS is now signed for upstream (-) and downstream (+) of TSS
  o Column added to indicate whether the geneset is enriched or depleted

CHANGES IN VERSION 0.9
----------------------

NEW FEATURES

  o Added support for reading BED files natively

BUG FIXES

  o Fixed bug where invalid geneset in chipenrich() wasn't detected properly

CHANGES IN VERSION 0.8
----------------------
BUG FIXES

  o Fixed crash when mappability contained an NA (will be removed from DB in future version)

CHANGES IN VERSION 0.7
----------------------

USER-VISIBLE CHANGES

  o Updated binomial test to sum gene locus lengths to get genome length and remove genes that are not present in the set of genes being tested
  o Updated spline fit plot to take into account mappability if requested (log mappable locus length plotted instead of simply log locus length)
  o Removed SAMPLEABLE_GENOME* constants since they are no longer needed
  o Updated help files to reflect changes to plot_spline_length and chipenrich functions

BUG FIXES

  o Fixed bug where results for multiple gene set types (e.g. doing BioCarta and KEGG together) were not sorted by p-value

CHANGES IN VERSION 0.6
----------------------

BUG FIXES

  o Fixed bug where 1kb/5kb locusdefs could fail if not all peaks were assigned to a gene

CHANGES IN VERSION 0.5
----------------------

USER-VISIBLE CHANGES

  o Updated help to explain new mappability model
  o Changed how mappability is handled - now multiplies gene locus length by mappability, rather than adjusting as a spline term
