cBioStudy: Retrieve data and annotations 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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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 [email protected]

See Also

listStudies, cBioDataSet, cBioNCviz


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