get_profile_data: Retrieve TCGA Data corresponding to a Specific Genetic...

View source: R/tcgaretriever_v_1_7.R

get_profile_dataR Documentation

Retrieve TCGA Data corresponding to a Specific Genetic Profile of Interest

Description

Retrieve Data corresponding to a Genetic Profile of interest from a study of interest. This function is the workhorse of the TCGAretriever package and can be used to fetch data concerning several genes at once. For larger queries, the use of the fetch_all_tcgadata() function is mandatory.

Usage

get_profile_data(
  case_id = "blca_tcga_all",
  gprofile_id = "blca_tcga_mutations",
  glist = c("TP53", "E2F1"),
  force_numeric = FALSE
)

Arguments

case_id

String corresponding to the Identifier of a list of cases

gprofile_id

String corresponding to the Identifier of a genetic Profile of interest

glist

Character vector including one or more gene identifiers (ENTREZID or OFFICIAL_SYMOL)

force_numeric

logical. Shall numeric data be coerced to numeric?

Value

data.frame with one row per gene and one column per case/sample

Author(s)

Damiano Fantini, damiano.fantini@gmail.com

References

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

Examples

get_profile_data("blca_tcga_all", "blca_tcga_mutations", c("TP53", "E2F1"))


TCGAretriever documentation built on July 26, 2023, 5:51 p.m.