Description Usage Arguments Value Author(s) Examples
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.
1 2 | select_database(database, MITAB_table, flag)
|
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" |
output |
iRefIndex/MITAB R table with the previously specified features. |
Antonio Mora <antoniocmora@gmail.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## 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")
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