get_mutation_data: Retrieve Mutation Data corresponding to a Genetic Profile of...

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

Retrieve Mutation Data corresponding to a Genetic Profile of Interest.

Description

Retrieve DNA Sequence Variations (Mutations) identified by exome sequencing projects. This function is the workhorse of the TCGAretriever package for mutation data and can be used to fetch data concerning several genes at once. For retrieving non-mutation data, please use the 'get_molecular_data()' function. For large queries (more than 500 genes), please use the 'fetch_all_tcgadata()' function.

Usage

get_mutation_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_SYMOL). 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 inluding one row per mutation

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_mutation_data(case_list_id = 'blca_tcga_sequenced',
                       gprofile_id = 'blca_tcga_mutations',
                       glist = c('TP53', 'PTEN'), dryrun = TRUE)
utils::head(x[, c(4, 7, 23, 15, 16, 17, 24, 18, 21)]) 
 

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