cBioStudy: Retrieve data and annotations 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

cBioStudy(study_id, genes_list = "http://acsn.curie.fr/files/acsn_v1.0.gmt",
  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
method	String, either "genes" or "profiles", specifying whether the data must be fetched by genes or by profiles. The result is the same but the "genes" version is more detailed.
url	URL to the CGDS API

Value

A list containing the annotations in a dataframe (sample_id * annotation_type) and the data. The format of the data depends on the method :
"genes" : a list (indexed by gene names) of dataframes (sample_id * profiling method)
"profiles" : a list (indexed by profiling methods) of dataframes (genes * samples), and the annotations in a dataframe (sample_id * annotation_type)

Author(s)

Mathurin Dorel [e-mail]

See Also

listStudies, cBioDataSet, cBioNCviz

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