NEWS

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UniProt.ws 2.50.0

SIGNIFICANT USER-VISIBLE CHANGES

• 'query' input in 'queryUniProt' can now be a named list; clarified in documentation

BUG FIXES AND MINOR IMPROVEMENTS

• 'collapse' in 'queryUniProt' does not need spaces padding, argument is not case-sensitive

UniProt.ws 2.48.0

SIGNIFICANT USER-VISIBLE CHANGES

• Switched to using the 'httr2' package for making HTTP requests
• Reorganized and renamed documentation for the 'UniProt.ws' class and its methods
• Converted unit testing framework from 'testthat' to 'tinytest'
• Added the 'README.md' file from the vignette
• Improved handling of API responses: empty results with code 200 are now caught and handled properly
• The 'collapse' argument in 'queryUniProt' now shows both 'OR' and 'AND' options

BUG FIXES AND MINOR IMPROVEMENTS

• Added an example to 'queryUniProt()'
• Fixed formatting issues in unit tests and corrected indentation in code
• Adjusted internal logic to support queries returning larger result sets
• Re-added 'Sys.sleep()' call to respect rate limits
• Set 'n' argument in internal use of 'head()'

UniProt.ws 2.46.0

BUG FIXES AND MINOR IMPROVEMENTS

• No significant changes.

UniProt.ws 2.44.0

BUG FIXES AND MINOR IMPROVEMENTS

• No significant changes.

UniProt.ws 2.42.0

NEW FEATURES

• 'pageSize' and 'n' arguments added to 'queryUniProt' to expose underlying API request defaults. It is recommended to set the pageSize to a large value e.g. 500 for large queries.

BUG FIXES AND MINOR IMPROVEMENTS

• Support for directly mapping to 'Ensembl' IDs with 'select'.
• Fixed issue with pagination with large queries (over 25 results) in 'queryUniProt' (@jdreyf, #23)

UniProt.ws 2.40.0

USER VISIBLE CHANGES

• Convert vignette from RSweave to web-based RMarkdown

BUG FIXES AND MINOR IMPROVEMENTS

• Increase fault tolerance of unit tests
• Add examples to 'mapUniProt' documentation

UniProt.ws 2.38.0

USER VISIBLE CHANGES

• 'UniProt.ws' uses the https://rest.uniprot.org/ API interface for queries.
• 'mapUniprot' is an exported function to directly map identifiers via UniProt and is used by the 'select' method.
• 'allToKeys' and 'allFromKeys' provide all the available 'to' and 'from' keys for mapping identifiers
• 'returnFields' provides all the possible inputs to the 'columns' argument in the 'select' and 'mapUniProt' functions (ids in the 'name' column)

UniProt.ws 2.27.0

BUG FIXES AND MINOR IMPROVEMENTS

• (2.27.1) Fix bug when selecting column GENEID. The mapping mapped both GENEID and ENTREZ_GENE to P_ENTREZGENE. When returning columsn used match to identify but would only pick up first match which was ENTREZ_GENE entry.

UniProt.ws 1.2.0

NEW FEATURES

• UniProt.ws creates an object that talks directly to the web services at UniProt. As such, it provides access to a tremendous library of IDs etc. directly from UniProt.
• When the package loads there will be acces to a Uniprot.ws object, this object has select, keys, cols and keytypes methods that behave the way these methods normally do for the other annotation packages.
• One important difference from other packages is that the user must use the species method to set the species to their organism of choice (by default it is set for humans). This is because the web resource is too big to return values for all these species at the same time. Uniprot currently has support for over 21,000 different species.
• Please see the manual pages and associated vignette for more detailed information about how to use this resource.