get_mutation_data {TCGAretriever} | R Documentation |
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, damiano.fantini@gmail.com
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)])