Perform identifier mapping using an existing column of supported identifiers to populate a new column with identifiers mapped to the originals.
mapTableColumn( column, species, map.from, map.to, force.single = TRUE, table = "node", namespace = "default", network = NULL, base.url = .defaultBaseUrl )
| column | Name of column containing identifiers of type specified by
|
|---|---|
| species | Common name for species associated with identifiers, e.g., Human. See details. |
| map.from | Type of identifier found in specified |
| map.to | Type of identifier to populate in new column. See details. |
| force.single | (optional) Whether to return only first result in cases of one-to-many mappings; otherwise the new column will hold lists of identifiers. Default is TRUE. |
| table | (optional) Name of table, e.g., node (default), edge or network |
| namespace | (optional) Namespace of table, e.g., default (default), shared or hidden |
| network | (optional) Name or SUID of the network. Default is the "current" network active in Cytoscape. |
| base.url | (optional) Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://localhost:1234 and the latest version of the CyREST API supported by this version of RCy3. |
dataframe with map.from and map.to columns. Beware: if map.to is not unique, it will be suffixed with an incrementing number in parentheses, e.g., if mapIdentifiers is repeated on the same network. However, the original map.to column will be returned regardless.
Supported species: Human, Mouse, Rat, Frog, Zebrafish, Fruit fly, Mosquito, Worm, Arabidopsis thaliana, Yeast, E. coli, Tuberculosis.
Supported identifier types (depending on species): Ensembl, Entrez Gene, Uniprot-TrEMBL, miRBase, UniGene, HGNC (symbols), MGI, RGD, SGD, ZFIN, FlyBase, WormBase, TAIR.
# \donttest{ mapped.cols <- mapTableColumn('name','Yeast','Ensembl','SGD') # name SGD #17920 YER145C S000000947 #17921 YMR058W S000004662 #17922 YJL190C S000003726 #... # }