get_ext_mutation: Retrieve Extended Information About DNA Mutations from TCGA

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

Retrieve Extended Information About DNA Mutations from TCGA

Description

Query TCGA for Data about DNA Sequence Variations (Mutations) identified by exome sequencing projects. The function will retrieve an extensive set of information for each mutation that was identified in the set of cases of interest. The function can only handle a limited number of query genes. For larger queries, use the fetch_all_tcgadata() function.

Usage

get_ext_mutation(
  case_id = "blca_tcga_sequence",
  gprofile_id = "blca_tcga_mutations",
  glist = c("TP53", "PTEN")
)

Arguments

case_id	string corresponding to the Identifier of the case_list of interest
gprofile_id	string corresponding to the Identifier of the Genetic Profile of Interest
glist	character vector including Gene Identifiers (ENTREZID or OFFICIAL_SYMBOL)

Value

data Frame inluding one row per mutation

Author(s)

Damiano Fantini, [e-mail]

References

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

Examples

my_case_id <- 'blca_tcga_sequence'
my_gprofile_id <- 'blca_tcga_mutations'
my_gene <- 'TP53'
tp53_mutats <- get_ext_mutation(my_case_id, my_gprofile_id, my_gene)
if(ncol(tp53_mutats) >= 6 & nrow(tp53_mutats) >= 10){
  tp53_mutats[1:10,1:6]
}

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