mapTableColumn {RCy3} | R Documentation

## Map Table Column

### Description

Perform identifier mapping using an existing column of supported identifiers to populate a new column with identifiers mapped to the originals.

### Usage

    mapTableColumn(
      column,
      species,
      map.from,
      map.to,
      force.single = TRUE,
      table = "node",
      namespace = "default",
      network = NULL,
      base.url = .defaultBaseUrl
    )

### Arguments

`column` | Name of column containing identifiers of type specified by `map.from`.
`species` | Common name for species associated with identifiers, e.g., Human. See details.
`map.from` | Type of identifier found in specified `column`. See details.
`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.

### Details

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.

### Value

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.

### Examples

    mapped.cols <- mapTableColumn('name','Yeast','Ensembl','SGD')
    #          name        SGD
    #17920  YER145C S000000947
    #17921  YMR058W S000004662
    #17922  YJL190C S000003726
    #...

[Package RCy3 version 2.6.3 Index]