CHANGES IN VERSION 1.15.1 ------------------------ BUG FIXES o Importing from S4Vectors instead of IRanges CHANGES IN VERSION 1.7.4 ------------------------ BUG FIXES o Removed import error introduced with version 1.7.2 CHANGES IN VERSION 1.7.3 ------------------------ BUG FIXES o Minor bug fix CHANGES IN VERSION 1.7.2 ------------------------ NEW FEATURES o annotatePeaks now assigns a gene to the peak center instead of the peak limits o annotatePeaks takes the new argument 'reference' to enable alternative peak to gene body associations CHANGES IN VERSION 1.7.1 ------------------------ BUG FIXES o Minor correction to avoid warning messages issued after GRanges to data.frame conversion CHANGES IN VERSION 1.5.9 ------------------------ BUG FIXES o Use of mcols in favor of values to access meta data in GRanges objects CHANGES IN VERSION 1.5.8 ------------------------ BUG FIXES o Minor bug fix in annotatePeaks to accommodate recent changes in GRanges CHANGES IN VERSION 1.5.7 ------------------------ BUG FIXES o Minor bug fix in annotatePeaks CHANGES IN VERSION 1.5.6 ------------------------ BUG FIXES o Minor bug fix CHANGES IN VERSION 1.5.5 ------------------------ BUG FIXES o Speed improvement and improved accuracy of annotatePeaks CHANGES IN VERSION 1.5.4 ------------------------ NEW FEATURES o plotTV can now plot expression profiles including introns triggered by the new option pre_mRNA BUG FIXES o Fixed a bug which occurred if only two colors were passed to plotTV via colr CHANGES IN VERSION 1.5.3 ------------------------ NEW FEATURES o meltPeak can return loess smoothed scores. CHANGES IN VERSION 1.5.2 ------------------------ BUG FIXES o Fixed an issue with the gene names returned from gtf2gr. CHANGES IN VERSION 1.5.1 ------------------------ BUG FIXES o The q-value cut off in macs2gr did not work as expected. CHANGES IN VERSION 1.2.11 ------------------------ BUG FIXES o Fixed a compilation problem related to the new Rsamtools version on windows. CHANGES IN VERSION 1.2.9 ------------------------ BUG FIXES o Updated vignette CHANGES IN VERSION 1.2.8 ------------------------ NEW FEATURES o meltPeaks() normalizes to Reads Per Million mapped reads after quality filtering according to the filtered_reads slot. o parseReads() now also returns the total and local base pairs covered which can be accessed by the slots gsize() and lsize() respectively. CHANGES IN VERSION 1.2.7 ------------------------ NEW FEATURES o New convenience function meltPeaks(), which returns a data frame with normalized peak densities suitable for plotting with ggplot2. BUG FIXES o Minor help file corrections. CHANGES IN VERSION 1.2.6 ------------------------ BUG FIXES o macs2gr() supports relative distances instead of absolute distances reported by older MACS versions. CHANGES IN VERSION 1.2.5 ------------------------ BUG FIXES o annotatePeaks() did not accurately resolve ambiguities in some instances. CHANGES IN VERSION 1.2.4 ------------------------ BUG FIXES o gtf2gr() can now handle gene and transcript IDs with white spaces. CHANGES IN VERSION 1.2.3 ------------------------ NEW FEATURES o All slice methods can now return binned densities of predefined width. o The method to bin data can be specified by a new option in plotTV and the slice methods called bin_method. The amount of bins to be returned can be specified by nbins. o Default method to plot densities in plotTV is now mean instead of linear interpolation using approx. median or max are additional possibilities. CHANGES IN VERSION 1.2.2 ------------------------ BUG FIXES o Minor bug fix in plotTV CHANGES IN VERSION 1.2.1 ------------------------ BUG FIXES o Minor bug fix in plotTVData CHANGES IN VERSION 1.2.0 ------------------------ NEW FEATURES o A new class TVResults is returned by plotTV containing all important results of the clustering and plotting. o TVResults objects can be accessed by their slots and plotTVData. plotTVData returns a data frame with the summarized results. o Added option showPlot to plotTV() to suppress plotting optionally. This is useful if only the clustering results are needed. o Added an option name_width to plotTV() to enable customized widths of the row labels. BUG FIXES o Improved kmeans clustering CHANGES IN VERSION 1.1.6 ------------------------ BUG FIXES o Fixed an error which occurred if annotatePeaks was used with unifyBy. o sliceNT did not flip the exons on the negative strand in some situations. CHANGES IN VERSION 1.1.5 ------------------------ NEW FEATURES o gtf2gr transcript_id and gene_id attribute names can now be customized. BUG FIXES o annotatePeaks returned an error when remove_unmatched was disabled. o Increased filter accuracy of annotatePeaks when min_genelength > 0. CHANGES IN VERSION 1.1.4 ------------------------ NEW FEATURES o All slice methods return NA instead of NULL in case of chromosome miss matches or negative query lengths. BUG FIXES o Using toRle in the slice methods will work with missing values. CHANGES IN VERSION 1.1.3 ------------------------ NEW FEATURES o Setting psize to 'preserve' will enable macs2gr to return the original peak lengths. o annotatePeaks can now preserve the gene_id column if present. BUG FIXES o Improved type checking. CHANGES IN VERSION 1.1.2 ------------------------ NEW FEATURES o Added an option to gtf2gr which defines the GTF feature type entry to be filtered during parsing o gtf2gr also incorporates the gene_id if present in the input gtf file CHANGES IN VERSION 1.1.1 ------------------------ BUG FIXES o Fixed a bug which resulted in wrong quality score cut off in parseReads() o annotatePeaks() did not accept input gtf files with present values CHANGES IN VERSION 1.1.0 ------------------------ BUG FIXES o Fixed a bug which resulted in wrong density maps of overlapping regions from sliceN NEW FEATURES o Release version with several minor, mainly manual related improvements. CHANGES IN VERSION 0.99.3 ------------------------ NEW FEATURES o Renamed all C files. Registering now takes place in a separate file. o plotTV can now alternatively take a character vector of IDs matching 'transcript_id' in the gtf instead of a GRanges object. This is useful to plot RNA-Seq data matching without regions. BUG FIXES o Added PACKAGE argument to .call o readthrough_pairs argument to parseReads declared experimental. o Removed the matching RNA-Seq data set and added pasillaBamSubset as an example for RNA-Seq visualisation. CHANGES IN VERSION 0.99.2 ------------------------ NEW FEATURES o Added getter methods for all slots of DensityContainer and inherited classes for individual access. Added setter methods for spliced and ex_name o removed dc.size() and added the slot 'size' instead. Also added env and data_pointer slots to class DensityContainer o improved documentation of S4 methods with usage section o gtf2df and macs2df renamed to gtf2gr and macs2gr respectively. They are now returning a GRanges object. o annotatePeaks takes and returns only GRanges objects. o id2tss renamed to peak2tss and now returning an updated GRanges object o plotTV accepts GRanges objects rather than data.frames for gtf and peaks input BUG FIXES o Removed all direct slot accessions o Removed unnecessary call to dyn.load and dyn.unload in parseReads() CHANGES IN VERSION 0.99.1 ------------------------ NEW FEATURES o plotTV returns ordering to reproduce kmeans clustering BUG FIXES o sliceNT did not flip the exons on the negative strand o Argument rowv to plotTV did not work with expression threshold remove_lowex o Installation on 32bit Windows was not possible