importStudy: Import a study from a file

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

Description

Import a study from a file with its annotations. A study consists of several experiments on the same set of genes and samples. For a study on m patients and n genes, the file must be formated as "M experiment_name", followed by a line with the list of samples ids, followed by n lines "genes_name data". The annotations start by "ANNOTATIONS study_name", followed by a line with the list of annotations names, followed by m lines "sample_name annotation".

Import a study from a file in an NCviz object.

Usage

importStudy(fname)

importNCviz(fname, nc_url = "http://acsn.curie.fr/files/acsn_v1.0.owl",
  cell_type = "guess")

Arguments

fname	Name of the file
nc_url	URL of the NaviCell server
cell_type	Name of the data. If cell_type == "guess", it will be deduced from the file name by default.

Value

A list (indexed by profiling methods) of dataframes (genes * samples), and the annotations in a dataframe (sample_id * annotation_type).

An NCviz object.

Author(s)

Mathurin Dorel [e-mail]

See Also

cBioStudy, saveData

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