cBioNCviz: Create NCviz object from a c-Bioportal study

In sysbio-curie/cBioFetchR: Extract data from cBioPortal in a way that they can easily be exported to NaviCell

Description

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

Usage

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 [e-mail]

See Also

listStudies, cBioDataSet, cBioStudy

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