NEWS

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TransView 1.15.1

BUG FIXES

• Importing from S4Vectors instead of IRanges

TransView 1.7.4

BUG FIXES

• Removed import error introduced with version 1.7.2

TransView 1.7.3

BUG FIXES

• Minor bug fix

TransView 1.7.2

NEW FEATURES

• annotatePeaks now assigns a gene to the peak center instead of the peak limits
• annotatePeaks takes the new argument 'reference' to enable alternative peak to gene body associations

TransView 1.7.1

BUG FIXES

• Minor correction to avoid warning messages issued after GRanges to data.frame conversion

TransView 1.5.9

BUG FIXES

• Use of mcols in favor of values to access meta data in GRanges objects

TransView 1.5.8

BUG FIXES

• Minor bug fix in annotatePeaks to accommodate recent changes in GRanges

TransView 1.5.7

BUG FIXES

• Minor bug fix in annotatePeaks

TransView 1.5.6

BUG FIXES

• Minor bug fix

TransView 1.5.5

BUG FIXES

• Speed improvement and improved accuracy of annotatePeaks

TransView 1.5.4

NEW FEATURES

• plotTV can now plot expression profiles including introns triggered by the new option pre_mRNA

BUG FIXES

• Fixed a bug which occurred if only two colors were passed to plotTV via colr

TransView 1.5.3

NEW FEATURES

• meltPeak can return loess smoothed scores.

TransView 1.5.2

BUG FIXES

• Fixed an issue with the gene names returned from gtf2gr.

TransView 1.5.1

BUG FIXES

• The q-value cut off in macs2gr did not work as expected.

TransView 1.2.11

BUG FIXES

• Fixed a compilation problem related to the new Rsamtools version on windows.

TransView 1.2.9

BUG FIXES

• Updated vignette

TransView 1.2.8

NEW FEATURES

• meltPeaks() normalizes to Reads Per Million mapped reads after quality filtering according to the filtered_reads slot.
• parseReads() now also returns the total and local base pairs covered which can be accessed by the slots gsize() and lsize() respectively.

TransView 1.2.7

NEW FEATURES

• New convenience function meltPeaks(), which returns a data frame with normalized peak densities suitable for plotting with ggplot2.

BUG FIXES

• Minor help file corrections.

TransView 1.2.6

BUG FIXES

• macs2gr() supports relative distances instead of absolute distances reported by older MACS versions.

TransView 1.2.5

BUG FIXES

• annotatePeaks() did not accurately resolve ambiguities in some instances.

TransView 1.2.4

BUG FIXES

• gtf2gr() can now handle gene and transcript IDs with white spaces.

TransView 1.2.3

NEW FEATURES

• All slice methods can now return binned densities of predefined width.
• 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.
• Default method to plot densities in plotTV is now mean instead of linear interpolation using approx. median or max are additional possibilities.

TransView 1.2.2

BUG FIXES

• Minor bug fix in plotTV

TransView 1.2.1

BUG FIXES

• Minor bug fix in plotTVData

TransView 1.2.0

NEW FEATURES

• A new class TVResults is returned by plotTV containing all important results of the clustering and plotting.
• TVResults objects can be accessed by their slots and plotTVData. plotTVData returns a data frame with the summarized results.
• Added option showPlot to plotTV() to suppress plotting optionally. This is useful if only the clustering results are needed.
• Added an option name_width to plotTV() to enable customized widths of the row labels.

BUG FIXES

• Improved kmeans clustering

TransView 1.1.6

BUG FIXES

• Fixed an error which occurred if annotatePeaks was used with unifyBy.
• sliceNT did not flip the exons on the negative strand in some situations.

TransView 1.1.5

NEW FEATURES

• gtf2gr transcript_id and gene_id attribute names can now be customized.

BUG FIXES

• annotatePeaks returned an error when remove_unmatched was disabled.
• Increased filter accuracy of annotatePeaks when min_genelength > 0.

TransView 1.1.4

NEW FEATURES

• All slice methods return NA instead of NULL in case of chromosome miss matches or negative query lengths.

BUG FIXES

• Using toRle in the slice methods will work with missing values.

TransView 1.1.3

NEW FEATURES

• Setting psize to 'preserve' will enable macs2gr to return the original peak lengths.
• annotatePeaks can now preserve the gene_id column if present.

BUG FIXES

• Improved type checking.

TransView 1.1.2

NEW FEATURES

• Added an option to gtf2gr which defines the GTF feature type entry to be filtered during parsing
• gtf2gr also incorporates the gene_id if present in the input gtf file

TransView 1.1.1

BUG FIXES

• Fixed a bug which resulted in wrong quality score cut off in parseReads()
• annotatePeaks() did not accept input gtf files with present values

TransView 1.1.0

BUG FIXES

• Fixed a bug which resulted in wrong density maps of overlapping regions from sliceN

NEW FEATURES

• Release version with several minor, mainly manual related improvements.

TransView 0.99.3

NEW FEATURES

• Renamed all C files. Registering now takes place in a separate file.
• 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

• Added PACKAGE argument to .call
• readthrough_pairs argument to parseReads declared experimental.
• Removed the matching RNA-Seq data set and added pasillaBamSubset as an example for RNA-Seq visualisation.

TransView 0.99.2

NEW FEATURES

• Added getter methods for all slots of DensityContainer and inherited classes for individual access. Added setter methods for spliced and ex_name
• removed dc.size() and added the slot 'size' instead. Also added env and data_pointer slots to class DensityContainer
• improved documentation of S4 methods with usage section
• gtf2df and macs2df renamed to gtf2gr and macs2gr respectively. They are now returning a GRanges object.
• annotatePeaks takes and returns only GRanges objects.
• id2tss renamed to peak2tss and now returning an updated GRanges object
• plotTV accepts GRanges objects rather than data.frames for gtf and peaks input

BUG FIXES

• Removed all direct slot accessions
• Removed unnecessary call to dyn.load and dyn.unload in parseReads()

TransView 0.99.1

NEW FEATURES

• plotTV returns ordering to reproduce kmeans clustering

BUG FIXES

• sliceNT did not flip the exons on the negative strand
• Argument rowv to plotTV did not work with expression threshold remove_lowex
• Installation on 32bit Windows was not possible