iRefR (version 1.13)

select_database: Select iRefIndex Records belonging to given Primary Interaction Databases

Description

Select the subset of records in iRefIndex belonging to one or a group of Primary Interaction Databases. In addition, select all records except for that database or those databases.

Usage

select_database(database, MITAB_table, flag)

Arguments

database

Name of the protein interaction DB or vector of databases to extract from iRefIndex (options: "intact", "bind", "bind_translation", "biogrid", "mint", "ophid", "mppi", "hprd", "dip", "corum", "mpact", "innatedb", "matrixdb", "mpi-lit", "mpi-imex"). Before iRefIndex 10.0, the BioGRID database was called "grid" and the "mpi-lit" and "mpi-imex" were called "mpilit" and "mpiimex" respectively.

MITAB_table

iRefIndex/MITAB R table.

flag

Either "this_database" to get all "database" records, or "except_this_database" to get all records except for the ones belonging to "database". Default="this_database"

Value

output

iRefIndex/MITAB R table with the previously specified features.

Examples

     ## get tables
     irefindex_curr_ecoli = get_irefindex("562", "13.0", tempdir())
     iRef_binary = select_interaction_type("binary", irefindex_curr_ecoli)
     iRef_complex = select_interaction_type("complex", irefindex_curr_ecoli)

     ## execute function
     binary_INTACT = select_database("intact", iRef_binary, "this_database")
     binary_non_INTACT = select_database("intact", iRef_binary, "except_this_database")
     complex_INTACT_mint = select_database(c("intact", "mint"), iRef_complex,
 "this_database")
     complex_non_INTACT_mint = select_database(c("intact", "mint"), iRef_complex,
 "except_this_database")