filter_epitopes: Filter epitopes by taxonomy and host
In fcampelo/epitopes: Processing and Feature Extraction for Epitope Data

filter_epitopes

R Documentation

Filter epitopes by taxonomy and host

Filters an epitope dataframe by source organism and/or host IDs.

filter_epitopes(
  df,
  orgIDs = NULL,
  hostIDs = NULL,
  removeIDs = NULL,
  tax_load_file = NULL,
  tax_list = NULL,
  tax_save_folder = NULL
)

`df`	data.table object of class LBCE_dt (generated by `get_LBCE()`), joined_epit_dt (generated by `prepare_join_df()`) or windowed_epit_dt (generated by `make_window_df()`)
`orgIDs`	vector of organism taxon IDs that we want to retain (using sourceOrg_id).
`hostIDs`	vector of host taxon IDs that we want to retain (using host_id).
`removeIDs`	vector of organism taxon IDs that we want to remove (using sourceOrg_id).
`tax_load_file`	optional taxonomy file (RDS file generated either by this function or by `get_taxonomy()`).
`tax_list`	optional taxonomy list (to be passed instead of tax_load_file)
`tax_save_folder`	optional folder saving the taxonomy. Ignored if tax_load_file is not NULL.