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CHANGES IN VERSION 1.11.4
-------------------------
PKG FEATURES
o Back-end refactoring of the code base.
o Break out functions in main.R into .R files collecting similar functions.
o Transition documentation to roxygen2 blocks.
o Improve commenting in chipenrich() function.
o Assigning peaks using GenomicRanges object rather than than list of IRanges.
o Rewrite package vignette in Rmarkdown and render with knitr.
o Improve supported_*() functions to report and check combinations of genome,
organism, genesets, locusdef, and mappability read length.
o Cleanup DESCRIPTION and NAMESPACE to avoid loading entire packages.
o Follow data() best practices.
CHANGES IN VERSION 1.3.4
------------------------
PKG FEATURES
o A new method, broadenrich, is available in the chipenrich function which is
designed for gene set enrichment on broad genomic regions, such as peaks resulting
from histone modificaiton based ChIP-seq experiments.
o Methods chipenrich and broadenrich are available in multicore versions (on every
platform except Windows). The user selects the number of cores when calling
the chipenrich function.
o Peaks downloaded from the ENCODE Consortium as .broadPeak or .narrowPeak files
are supported directly.
o Peaks downloaded from the modENCODE Consortium as .bed.gff or .bed.gff3 files are
also supported directly.
o Support for D. melanogaster (dm3) genome and enrichment testing for GO terms
from all three branches (GOBP, GOCC, and GOMF).
o New gene sets from Reactome (http://www.reactome.org) for human, mouse, and rat.
o New example histone data set, peaks_H3K4me3_GM12878, based on hg19.
o New locus definitions including: introns, 10kb within TSS, and 10kb upstream of TSS.
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