cBioNCviz: Create NCviz object from a c-Bioportal study

Description Usage Arguments Value Author(s) See Also

Description

Retrieve data and annotations from a c-Bioportal study and select genes that are present on the NaviCell map

Usage

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cBioNCviz(study_id, genes_list = "http://acsn.curie.fr/files/acsn_v1.0.gmt",
  nc_url = "http://acsn.curie.fr/files/acsn_v1.0.owl", name = "",
  method = "profiles", url = "http://www.cbioportal.org/")

Arguments

study_id

ID of the study to retrieve.

genes_list

URL pointing to the list of genes of interest (in .gmt format), or a list of genes HUGO identifiers

nc_url

URL of the NaviCell map

name

Name of the dataset. If not provided, the name of the study provided by cBioPortal will be used

method

String, either "genes" or "profiles", specifying whether the data must be fetched by genes or by profiles. The result is the same, however the "genes" version is more detailed but much slower and uses more memory.

url

URL to the CGDS API

Value

An NCviz object containing the data of the study

Author(s)

Mathurin Dorel [email protected]

See Also

listStudies, cBioDataSet, cBioStudy


sysbio-curie/cBioFetchR documentation built on May 31, 2019, 12:48 a.m.