cBioDataSet: Retrieve a dataset from c-Bioportal

Description Usage Arguments Details Value Author(s) See Also

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

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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 [email protected]

See Also

cBioStudy, importDataSet, saveData


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