TCGAretriever (version 1.9.1)

fetch_all_tcgadata: 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)

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

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

Author

Damiano Fantini,

References

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

Examples

# The examples below require an active Internet connection.
# Note: execution may take several minutes.
if (FALSE) {
# 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)
}