Description Usage Arguments Details Value Examples
Perform identifier mapping using an existing column of supported identifiers to populate a new column with identifiers mapped to the originals.
1 2 3 4 5 6 7 8 9 10 11 | 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. |
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.
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.
1 2 3 4 5 6 | mapped.cols <- mapTableColumn('name','Yeast','Ensembl','SGD')
# name SGD
#17920 YER145C S000000947
#17921 YMR058W S000004662
#17922 YJL190C S000003726
#...
|
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