Convert Gene IDs Between Each Other and Fetch Annotations from Biomart
Convert Symbols to Aliases and Vice Versa.
Retrieve Additional Annotations from Biomart
Convert Gene IDs Between Each Other and Fetch Annotations from Biomart
Convert Gene Symbols to Ensembl Gene IDs or vice versa
Add values to cache
Unexported functions Test if a path exists and is writable
Check whether value in cache exists
Unexported functions Create a file cache directory at a given location...
Unexported functions Test and retrieve Ensembl-specific CURL SSL confi...
Unexported functions Get httr configuration, i.e., current CURL option...
Read values from cache
Unexported functions Set the location for the biomaRt cache
Make a Query to Biomart.
Retrieve Symbol Aliases and Previous symbols to determine a likely cur...
Convenience Function to Convert Ensembl Gene IDs to Gene Symbols
Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but that function is only provided as fallback mechanism 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.