Convert Gene IDs Between Each Other and Fetch Annotations from Biomart

Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol() attempts to determine the most likely current Gene Symbol.


Reference manual

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install.packages("convertid")

0.4.0 by Vidal Fey, 2 months ago


https://github.com/vfey/convertid


Report a bug at https://github.com/vfey/convertid/issues


Browse source code at https://github.com/cran/convertid


Authors: Vidal Fey [aut, cre] , Henrik Edgren [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports AnnotationDbi, plyr, stringr, biomaRt, stats, xml2, utils, rappdirs, assertthat, methods, httr, BiocFileCache

Suggests BiocManager, org.Hs.eg.db, org.Mm.eg.db, testthat, mockery, curl


Imported by coreheat, diffwrap.


See at CRAN