fetch_all_tcgadata {TCGAretriever}

Fetch All Molecular Data for a Cancer Profile of Interest.

Description

Recursively query cbioportal to retrieve data corresponding to all available genes. Data are returned as a 'data.frame' that can be easily manipulated for downstream analyses.

Usage

fetch_all_tcgadata(case_list_id, gprofile_id, mutations = FALSE)

Arguments

case_list_id

string corresponding to the identifier of the TCGA Case List of interest

gprofile_id

string corresponding to the identifier of the TCGA Profile of interest

mutations

logical. If TRUE, extended mutation data are fetched instead of the standard TCGA data

Value

A data.frame is returned, including the desired TCGA data. Typically, rows are genes and columns are cases. If "extended mutation" data are retrieved (mutations = TRUE), rows correspond to individual mutations while columns are populated with mutation features

Author(s)

Damiano Fantini, [e-mail]

References

https://www.data-pulse.com/dev_site/TCGAretriever/

Examples

# The examples below require an active Internet connection.
# Note: execution may take several minutes.
## Not run: 
# Download all brca_pub mutation data (complete samples)
all_brca_MUT <- fetch_all_tcgadata(case_list_id = "brca_tcga_pub_complete", 
                                   gprofile_id = "brca_tcga_pub_mutations", 
                                   mutations = TRUE)

# Download all brca_pub RNA expression data (complete samples)
all_brca_RNA <- fetch_all_tcgadata(case_list_id = "brca_tcga_pub_complete", 
                                   gprofile_id = "brca_tcga_pub_mrna", 
                                   mutations = FALSE)

## End(Not run)