Changes in version 1.31.2 (2024-07-05) Bug fix o Fix tSVE() shiny application. Changes in version 1.31.1 (2024-07-04) Bug fix o Copy parseCSQToGRanges from ensemblVEP Changes in version 1.19.1 (2021-08-30) Bug fix o Substitute || by |. Changes in version 1.13.2 (2020-04-11) Bug fix o tSVE vignette output format set to HTML. Changes in version 1.13.1 (2020-03-26) Bug fix o parallelSlotNames() was renamed vertical_slot_names() in S4Vectors 0.25.14. Changes in version 1.9.2 (2019-02-20) Bug fix o Fixes to pass updated BiocCheck requirements. Changes in version 1.5.4 (2017-09-24) Bug fix o min(ranges(GRanges)) does not seem to work anymore, replaced by more explicit expression. o Commented out some unit tests until subsetting of FilterRules by row _and_ column throws an error again. Changes in version 1.3.2 (2017-09-02) Bug fix o Updated vignette output format for compatibility with BiocStyle (>= 2.5.19); one vignette turned to PDF to respect the package size limit in the new context. Changes in version 1.3.1 (2017-05-30) Bug fix o Fixed VCF import from multiple files in _Shiny_ application. Changes in version 1.1.12 (2017-04-10) Major changes o Update GRangesFilter following update of the condition argument to type. Changes in version 1.1.11 (2017-04-08) Major changes o Update NAMESPACE imports following move of GRangesFilter and GenenameFilter from AnnotationFilter to ensembldb. Changes in version 1.1.10 (2016-11-18) Bug fix o Disambiguated the variable metric that was used for two different things in the same method and produced incorrect DataTrack name in plotInfo. Major changes o Vignette uses alternate allele frequency to demonstrate pairsInfo and plotInfo methods. Changes in version 1.1.9 (2016-11-18) Major changes o New argument zero.rm in method plotInfo to hide data points with value of zero on the Y axis. Intended to reduce overplotting of variants absent from phenotype levels, and instead emphasise variants of low frequency. Changes in version 1.1.8 (2016-11-14) New features o New method pairsInfo to visualise a matrix of pairwise plots that displays a metric calculated in levels of a given phenotype, and stored in columns of the info slot of a VCF object. o ggpairs method imported from the GGally package. Bug fix o Updated pattern used to detect INFO columns for a given metric, to be more specific. Major changes o Internal method .findInfoMetricColumns moved to utils.R, as it is now used in two different user-visible methods. o Updated Introduction vignette to better present usage of the addFrequencies method, better present _VCF filter rules_, and introduce the new method pairsInfo. Changes in version 1.1.7 (2016-11-11) Major changes o Plotting type(s) cab be selected for the DataTrack of plotInfo. Minor changes o Update to README. o _AppVeyor_ caches R library. Changes in version 1.1.6 (2016-11-10) New features o plotInfo method to visualise a metric calculated in levels of a given phenotype, and stored in columns of the info slot. o Methods imported from Gviz package. o More methods imported from ensembldb package. Major changes o Added new VCF file and associated preprocessing script in extdata/ for gene ADH1B. o Introduction vignette updated to change activated filter rules. o Introduction vignette updated to introduce the plotInfo method. Minor changes o Moved content of the table of motivations to implement _VCF filter rules_ to a CSV file in misc/. o BED file and VCF files for gene ADH1B. o Updated Shell script to preprocess VCF files with the VEP script. o Ignore .svn/. Changes in version 1.1.5 (2016-11-08) Bug fix o Updated reference to renamed object in _Shiny_ app. o When no phenotypes are supplied, set phenoData slot to a DataFrame with rownames set to colnames(vcf) and 0 columns, instead of the default behaviour of the VariantAnnotation package which is to create a column named Sample filled with seq_along. o NEWS file closing brackets. Major changes o autodetectGTimport setting available in tSVE method. o New checkbox in _Shiny_ app to update selected genotypes after importing variants and autodetection of genotypes present in the data. Minor changes o Do not ignore *.Rproj files. o Removed commented lines in _AppVeyor_ YAML file. o Removed files in misc/. o Display list of error messages in a new session panel of the _Shiny_ app. Changes in version 1.1.4 (2016-11-04) Bug fix o Bumped version number to try and update the Bioconductor GitHub mirror to display the latest code instead of version 0.1.7. Minor changes o Added TVTB.Rproj to tracked files. o Deleted deprecated and misc files in inst/. o Deleted commented lines from AppVeyor settings. Changes in version 1.1.3 (2016-11-03) New features o The autodetectGenotypes method creates or updates the genotypes defined in the TVTBparam that is stored in the metadata slot of a VCF object. o The argument autodetectGT of the readVcf method may be used to call the new autodetectGenotypes method immediately after a VCF object is initialised from the parsed VCF file. Major changes o vepInPhenoLevel returns a GRanges instead of a data.frame; the key advantage is that ranges may have non-unique names. o Genotypes objects can now be initialised without specifying ref, het, and alt genotype vectors (with a warning). A default Genotypes object is created with ref, het, and alt slots set to NA_character_. The new autodetectGenotypes method may be used to populate those slots after variants are imported (see _New features_ section). o TVTBparam objects can now be initialised without supplying a Genotypes object (with a warning). A default Genotypes object is created (see above). o Constructors for classes Genotypes and TVTBparam are now high-level methods, *not* S4 methods methods anymore. o Default settings of the _Shiny_ app are stored as an environment that can be overriden by arguments of the tSVE method. o _Shiny_ app stores more objects in reactiveValues. o _Shiny_ app stores more error messages in reactiveValues to better deal with optional inputs and better help users to resovle sources of errors. Minor changes o The show method throws warning messages for TVTBparam and Genotypes objects that have not fully defined all genotypes. o Better layout of badges in README. o Non-reactive settings of the _Shiny_ app stored in hidden objects. o Helper methodS getEdb, tryParsePheno, tryParseBed, tryParseVcfHeader, tryParseMultipleVcf, and tryParseSingleVcf removed and integrated into the server side of the _Shiny_ app. o Massive cleaning of messages in the global.R file of the _Shiny_ app. o GRanges, Genotypes, and Phenotypes panels removed from Session panel of the _Shiny_ app. o Table reporting status of BiocParallel configurations of the _Shiny_ app on various system stored as an RDS file. o _Shiny_ app displays a warning at the top of the screen if the genotypes are not fully defined. o Tab width of _Shiny_ files set to 2. o Branches tracked by Travis CI. o Added a couple of files in inst/badexamples folder. o Added YAML file for _AppVeyor_. o Added pander in Suggests section of DESCRIPTION, to render vignette tables. Changes in version 1.1.2 (2016-10-21) Minor changes o README indicates status on BioC-release, BioC-devel, and Travis CI. Changes in version 1.1.1 (2016-10-21) Minor changes o Updates to README: weblinks, installation, unit tests. o Branches tracked by Travis CI. o Coverage: exclude AllClasses.R, tSVE.R. o Four-space indents in DESCRIPTION. Changes in version 0.99.9 (2016-10-14) Minor changes o Fixed outdated information in _Introduction_ vignette. Changes in version 0.99.8 (2016-10-12) Minor changes o Set vignette output format to BiocStyle::html_document2. Changes in version 0.99.7 (2016-10-12) Minor changes o Fixed a closign bracket in NEWS file. Changes in version 0.99.6 (2016-10-12) Experimental changes o Replaced BiocStyle::pdf_document2() by BiocStyle::pdf_document(); the former fails at the pandoc step of vignette production, the latter does not. Changes in version 0.99.5 (2016-10-12) Bug fix o Fixed Collate: field of the DESCRIPTION file. Changes in version 0.99.4 (2016-10-12) Experimental changes o Reverted changes applied in version 0.99.3. BiocParallel does not seem to be causing the build error on Windows Server. Changes in version 0.99.3 (2016-10-12) Experimental changes o Disabled BiocParallel code to see if it resolves build errors on the _Bioconductor_ Windows Server. Note that the documentation was not yet updated to reflect this experimental change; this is intended to facilitate code reversion-or alternatively document the change-in the next commit. Changes in version 0.99.2 (2016-10-11) Bug fixes o Use suffix accessor in add*Frequencies methods. Changes in version 0.99.1 (2016-10-10) Major changes o New dedicated Genotypes class to store homozygote reference, heterozygote, and homozygote alternate genotype codes, along with the suffixes that define the INFO keys used to store their respective data in the VCF object. o Removed families of methods tabulate* and density* from the NAMESPACE. The features may be revisited in the future. The associated code and documentation was saved in the inst/sandbox subfolder for future reference. o New slot svp in TVTBparam class to store ScanVcfParam objects. New associated accessor methods. Moreover, TVTBparam may be coerced to ScanVcfParam. o New signatures for method readVcf that supports param=TVTBparam, and optional phenotypes. The method stores TVTBparam in the metadata slot of the VCF object, and phenotypes using the colData accessor. o TVTBparam are no longer an argument of downstream methods; instead, they must be stored in metadata(vcf)[["TVTBparam"]] Minor changes o hRef and hAlt accessors renamed to refand alt, respectively. o suffix accessor to returned named character vector for classes Genotypes and TVTBparam. o Removed functions relevant only to the _Shiny_ application from the NAMESPACE (getEdb, EnsDbFilter, chr2file). o VcfFilterRules can also store instances of the parent FilterRules class. o Defined default return value for accessors vep and type, to avoid unnecessary switch statements. o Simplified code of inherited methods following updates to the relevant packages (_e.g._ S4Vectors). o Better respect of coding standards: removed superfluous usage of explicit argument naming, removed superfluous initialize methods. o Man pages, vignettes, unit tests and _Shiny_ application updated to reflect changes to the package. Changes in version 0.99.0 (2015-09-15) New features o First release submitted to the Bioconductor review process See DESCRIPTION file for details.