TCGAretriever (version 1.7)

fetch_all_tcgadata: Recursively Fetch All Data Included in a TCGA Study Subset

Description

Recursively query TCGA to retrieve large volumes of data corresponding to a high number of genes (up to the entire genome). Data are returned as a data frame that can be easily manipulated for further analyses.

Usage

fetch_all_tcgadata(
  case_id = "blca_tcga_sequenced",
  gprofile_id = "blca_tcga_mutations",
  glist = c("PTEN", "TP53"),
  mutations = FALSE,
  force_numeric = 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_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

glist

character vector including one or more gene identifiers (ENTREZID or the OFFICIAL SYMBOL can be used)

mutations

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

force_numeric

logical. Shall columns including numeric values be coerced to numeric.

Author

Damiano Fantini,

References

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

Examples

# Mutations occurring on TP53 and PTEN genes in the bladder cancer study
# Returns 1 data frame: rows = genes; columns = cases
x <- fetch_all_tcgadata("blca_tcga_mutations", "blca_tcga_mutations", 
                        c("PTEN", "TP53"), mutation = FALSE)
# Extended mutations occurring on TP53 and PTEN genes in the bladder cancer study
# Returns 1 data frame: rows = mutations; columns = extended information
fetch_all_tcgadata("blca_tcga_all", "blca_tcga_mutations", c("PTEN", "TP53"), mutation = TRUE)