Creates an updated version of the homologene database. This is done by downloading
the latest gene annotation information and tracing changes in gene symbols and
identifiers over history. homologeneData2 was created using
this function over the original homologeneData. This function
requires downloading large amounts of data from the NCBI ftp servers.
updateHomologene(destfile = NULL,
baseline = homologene::homologeneData2, gene_history = NULL,
gene_info = NULL)Optional. Path of the output file.
The baseline homologene file to be used. By default uses the
homologeneData2 that is included in this package. The more ids
to update, the more time is needed for the update which is why the default option
uses an already updated version of the original database.
A gene history data frame, possibly returned by getGeneHistory
function. Use this if you want to have a static gene_history file to update up to a specific date.
An up to date gene_history object can be set to update to a specific date by trimming
rows that have recent dates. Note that the same is not possible for the gene_info
If not provided, the latest file will be downloaded.
A gene info data frame that contatins ID-symbol matches,
possibly returned by getGeneInfo. Use this if you
want a static version. Should be in sync with the gene_history file. Note that there is
no easy way to track changes in gene symbols back in time so if you want to update it up
to a specific date, make sure you don't lose that file.
Homologene database in a data frame with updated gene IDs and symbols