NEWS

GenomicScores 2.16.0

Added support to the latest version v4.0 of gnomAD MAF data, stored in the package MafH5.gnomAD.v4.0.GRCh38.
Updated vignette to showcase the use of pathogenicity score sets from AlphaMissense, as well as the latest gnomAD v4.0 MAF data.

Added four new pathogenicity score sets and corresponding metadata for hg19 and hg38: AlphaMissense.v2023.hg19, AlphaMissense.v2023.hg38, cadd.v1.6.hg19 and cadd.v1.6.hg38.
Updated vignette.

Added two new score sets and corresponding metadata for mm39: phastCons35way.UCSC.mm39 and phyloP35way.UCSC.mm39.
Added new method 'wgscores()' to find which genomic scores are present in a given set of genomic ranges. Feature request by https://github.com/rcastelo/GenomicScores/issues/20
Improved error messages about optional arguments without name or with a mispecified name in the call to 'gscores()'.

Added support to the latest version 3.1.2 of gnomAD MAF data, stored in the package MafH5.gnomAD.v1.1.2.GRCh38.

Bugfix on a problem caused by unordered input genomic ranges of width larger than 1, whose result was return in the wrong order; see https://github.com/rcastelo/GenomicScores/issues/18
Bugfix when accessing multiple populations of scores stored on an HDF5 backend.

Added a shiny app available through the function 'igscores()'.
Added support for genomic score packages (e.g., MafH5.*) that use HFD5 files as a backend.
Added a new function 'rgscores()' for randomly sampling genomic scores.

Added support to latest release 3.0 of gnomAD MAF data, stored in the package MafDb.gnomAD.r3.0.GRCh38.
Individual allele frequencies can be now retrieved from MafDb.* packages when 'ref' and 'alt' arguments are given to the functions 'gscores()' and 'score()'. See manual pages and vignette for further details.
NonSNRs are now searched giving the argument type="equal" to findOverlaps(). This means that only scores from exact matches to nonSNRs are returned.

Bugfix on the 'getGScores(') function that precluded accessing the files downloaded by the AnnotationHub
Bugfix in accessing MAF values from nonSNVs when multiallelic variants are stored in different records from the VCF file.

Added support to latest release 2.1 of gnomAD MAF data lifted to GRCh38 by Ensembl, stored in packages MafDb.gnomAD.r2.1.GRCh38 and MafDb.gnomADex.r2.1.GRCh38.

Bugfix in the support to TOPMED MAF data, to discard variants whose VCF FILTER is not set to PASS.

Functions and classes deprecated in the previous release (scores, MafDb class) have been now removed from the package.
Added support to latest release 2.1 of gnomAD MAF data, stored in packages MafDb.gnomAD.r2.1.hs37d5 and MafDb.gnomADex.r2.1.hs37d5.

The function 'scores()' has been deprecated and replaced by the function 'gscores()'.
The argument 'scores.only' in the function 'scores()' has been deprecated and replaced by calling the function 'score()'.
The 'MafDb' class has been deprecated and now the 'GScores' class supports former 'MafDb' objects. The 'mafByOverlaps()' and 'mafById()' functions have been deprecated and replaced by the function 'gscores()'. The 'populations()' function from the 'MafDb' API has been integrated into the 'GScores' API.
Added metadata on genomic scores categories, available through the function 'gscoresCategory()', on availability of non-single nucleotide regions through the function 'gscoresNonSNRs()', and on the default population used through the function 'defaultPopulation()'.
New AnnotationHub resources have been added during this release cycle: phyloP60way.UCSC.mm10, LINSIGHT, phastCons46wayPlacental, phastcons46wayPrimates.
Added a BiocSticker at https://github.com/Bioconductor/BiocStickers/tree/master/GenomicScores
Added citation information after package publication has been accepted at Bioinformatics.

Added methods 'name()' and 'type()' for GScores objects.
Enabled the retrieval of multiple score values per genomic position (e.g., as in CADD or M-CAP scores).
Added method 'citation()' to fetch citation information for genomic scores.
Added function 'makeGScoresPackage()' to create an annotation package from an AnnotationHub genomic scores resource.
Added 'qfun()' and 'dqfun()' methods to fetch the quantization and dequantization functions from used to store and retrieved genomic scores.
Added 'quantized' argument to the 'scores()' method to obtain quantized values if the user wants to dequantize the values him or herself.
Fallback to local AnnotationHub when there is no internet connection to fetch genomic scores through AnnotationHub resources.
Added 'MafDb' class, derived from 'GScores' to store and access minor allele frequency values. This was originally defined in the 'VariantFiltering' package.
The vignette has been updated to illustrate the use of some of the previous changes.

Submission of the first version to the Bioconductor project. (start date: March 17, 2017)