Update homologene database

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)

Arguments

destfile	Optional. Path of the output file.
baseline	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.
gene_history	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.
gene_info	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.

Value

Homologene database in a data frame with updated gene IDs and symbols