NEWS

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gwasrapidd 0.99.17 (2023-12-15)

• Fixed issue #45
• Fixed documentation of traits()

gwasrapidd 0.99.16

• Fixed issue #46

gwasrapidd 0.99.15

• Fixed issue #41
• Update http mocks

gwasrapidd 0.99.14

• Merged pull request #37.

gwasrapidd 0.99.13

• Update pkgdown documentation to use template bootstrap 5.
• Regenerated precompiled vignettes.

gwasrapidd 0.99.11

• Fixed issues #8, #14, #16 and #17.
• Added identifier mapping functions: study_to_association(), study_to_variant(), study_to_trait(), association_to_study(), association_to_variant(), association_to_trait(), variant_to_study(), variant_to_association(), variant_to_trait(), trait_to_study(), trait_to_association(), and trait_to_variant().

gwasrapidd 0.99.10

• Fixed issue #13.

gwasrapidd 0.99.9

• gwasrapidd depends now on tidyr (> 0.8.99).

gwasrapidd 0.99.8

• genomic_contexts of object variants includes now the column is_mapped_gene.

gwasrapidd 0.99.7

• Addressing remaining warnings in Windows build, namely those related to broken doc links: https://github.com/Bioconductor/Contributions/issues/1124#issuecomment-499088435

gwasrapidd 0.99.6

• Addressing issue: https://github.com/Bioconductor/Contributions/issues/1124#issuecomment-499046949

gwasrapidd 0.99.5

• Just a version bump to troubleshoot bioc build on Windows: https://github.com/Bioconductor/Contributions/issues/1124#issuecomment-497415961.

gwasrapidd 0.99.4

• Added function open_in_gwas_catalog().

gwasrapidd 0.0.1

• Updated gwasrapidd packaging to comply with Bioconductor guidelines (BiocCheck::BiocCheck()).

gwasrapidd 0.0.0.9015

• Fixed typo in cheatsheet.

gwasrapidd 0.0.0.9014

• get_variants() can now use the cytogenetic_band criterion.

gwasrapidd 0.0.0.9013

• Added the dataset cytogenetic_bands.

gwasrapidd 0.0.0.9012

• Updated README installation command to use the new remotes package.
• Devel version badge is now hardcoded directly instead of using a call to badger.

gwasrapidd 0.0.0.9011

• get_variants() now accepts a new parameter: std_chromosomes_only. This allows to select whether variants mapped to scaffolds other than the standard chromosomes are returned. By default, now, get_variants() only returns variants mapped to chromosomes 1 thru 22, X, Y, or MT. This behaviour is now in line with results returned by the Web UI.
• Fixed bug with multiple_snp_haplotype and snp_interaction. NA values in columns multiple_snp_haplotype and snp_interaction of associations tibble in associations S4 object were being mapped to character type instead of logical. This is now fixed.
• Constructors for GWAS Catalog S4 objects ensure no NAs are in primary keys.
• Increased test coverage.

gwasrapidd 0.0.0.9010

• Changed type of column association_id in the S4 class associations from integer() to character(). This saves us from unnecessary coercions from integer to character when searching by association identifiers.
• The cheatsheet is also changed to reflect this update.

gwasrapidd 0.0.0.9009

• Added function exists_variant().

gwasrapidd 0.0.0.9008

• Improved the Getting Started vignette.

gwasrapidd 0.0.0.9007

• Added two new functions: open_in_dbsnp() and open_in_gtex().

gwasrapidd 0.0.0.9006

• Added a cheatsheet.

gwasrapidd 0.0.0.9005

• Improved test coverage significantly.

gwasrapidd 0.0.0.9004

• Reorganized mock fixtures. Now mock file paths are all under 100 chars. No more R CMD check whining.

gwasrapidd 0.0.0.9003

• Reference documentation is organized in the website.