get_molecular_data: Retrieve Molecular Data corresponding to a Genetic Profile of...

In dami82/TCGAretriever: Retrieve Genomic and Clinical Data from CBioPortal Including TCGA Data

Retrieve Molecular Data corresponding to a Genetic Profile of Interest.

Description

Retrieve Data corresponding to a Genetic Profile of interest from a cancer 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 retrieving mutation data, please use the 'get_mutation_data()' function. For large queries (more than 500 genes), please use the 'fetch_all_tcgadata()' function.

Usage

get_molecular_data(
  case_list_id,
  gprofile_id,
  glist = c("TP53", "E2F1"),
  dryrun = FALSE
)

Arguments

case_list_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	Vector including one or more gene identifiers (ENTREZID or OFFICIAL_SYMBOL). ENTREZID gene identifiers should be passed as numeric.
dryrun	Logical. If TRUE, all other arguments (if any) are ignored and a representative example is returned as output. No Internet connection is required for executing the operation when 'dryrun' is TRUE.

Value

data.frame including the molecular data of interest. Rows are genes, columns are samples.

Author(s)

Damiano Fantini, [e-mail]

References

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

Examples

# Set `dryrun = FALSE` (default option) in production!
x <- get_molecular_data(case_list_id = 'blca_tcga_3way_complete',
                        gprofile_id = 'blca_tcga_rna_seq_v2_mrna',
                        glist = c("TP53", "E2F1"), dryrun = TRUE)
x[, 1:10]

dami82/TCGAretriever documentation built on Feb. 2, 2024, 12:06 p.m.