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. 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