mapTableColumn: Map Table Column

In cytoscape/RCy3: Functions to Access and Control Cytoscape

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
#...

cytoscape/RCy3 documentation built on Nov. 1, 2024, 2:49 a.m.