Description Usage Arguments Value Author(s) Examples
Get all iRefIndex records for a given protein.
1 2 | select_protein(id_type, id_value, MITAB_table, complex_info)
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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". |
output |
iRefIndex/MITAB R table. |
Antonio Mora <antoniocmora@gmail.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | ## 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)
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