iRefR (version 1.13)

select_protein: Get all iRefIndex records for a given Protein

Description

Get all iRefIndex records for a given protein.

Usage

select_protein(id_type, id_value, MITAB_table, complex_info)

Arguments

id_type

Protein ID type ("irog" for iRefIndex's protein iROG ID; "icrog" for the canonical version of the iRefIndex's protein iROG ID; "uid" for iRefIndex's protein UID, which is formed of mainly UniProt IDs, followed by RefSeq IDs when there is no known UniProt ID and iROG IDs in case no UniProt or RefSeq are known).

id_value

A value or a vector of values of the iROG, icROG or UID to search for in a given iRefIndex/MITAB table.

MITAB_table

iRefIndex/MITAB R table.

complex_info

Flag that gives the user the option to retrieve either all the records of the complex to which such protein belongs to ("full_complex"), or only the record of the complex where the given protein is present ("not_full_complex"). Default="full_complex".

Value

output

iRefIndex/MITAB R table.

Examples

     ## Not run: 
#      ## get tables
#      irefindex_80_mouse = get_irefindex("10090", "8.0", tempdir())
# 
#      ## single queries
#      output_1 = select_protein("irogid", "4374882", irefindex_80_mouse,
#  "not_full_complex")
#      output_2 = select_protein("icrogid", "4374882", irefindex_80_mouse,
#  "not_full_complex")
#      output_3 = select_protein("icrogid", "2892004", irefindex_80_mouse,
#  "not_full_complex")
#      output_4 = select_protein("icrogid", "2892004", irefindex_80_mouse,
#  "full_complex")
#      output_5 = select_protein("icrogid", "1365685", irefindex_80_mouse,
#  "not_full_complex")
#      output_6 = select_protein("icrogid", "1365685", irefindex_80_mouse,
#  "full_complex")
# 
#      ## getting list of tables
#      irog_list = c("1828087", "2892004", "1365685")
#      table_list = list()
#      for (i in irog_list) {
#      	table_list[[i]] = select_protein("irogid", i, irefindex_80_mouse,
#  "not_full_complex")
#      }
# 
#      ## getting single table
#      irog_list = c("1828087", "2892004", "1365685")
#      table_single = select_protein("irogid", irog_list, irefindex_80_mouse,
#  "not_full_complex")
#      ## End(Not run)