cBioDataSet: Retrieve a dataset from c-Bioportal

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

Description

Retrieve a dataset from c-Bioportal for all genes that are present on the NaviCell map. Displays whether the NaviCell map genes have been included or not.

Usage

cBioDataSet(conn, study_id, profile_ids, case_id,
  genes_list = "http://acsn.curie.fr/files/acsn_v1.0.gmt",
  method = "profiles")

Arguments

conn	A CGDS connexion object
study_id	ID of the study to retrieve.
case_id	ID of the list of cases we want 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, however the "genes" version is more detailed but much slower and uses more memory.
profile_id	List of ids of the profiles we want to retrieve

Details

The method "profiles" does not work it there are too many samples

Value

The format 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

cBioStudy, importDataSet, saveData

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