fetch_all_tcgadata {TCGAretriever} | R Documentation |
Recursively query TCGA to retrieve large volumes of data corresponding to a high number of genes (up to the entire genome). Data are returned as a data frame that can be easily manipulated for further analyses.
fetch_all_tcgadata(
case_id = "blca_tcga_sequenced",
gprofile_id = "blca_tcga_mutations",
glist = c("PTEN", "TP53"),
mutations = FALSE,
force_numeric = FALSE
)
case_id |
string corresponding to the identifier of the TCGA Case List of interest |
gprofile_id |
string corresponding to the identifier of the TCGA Profile of interest |
glist |
character vector including one or more gene identifiers (ENTREZID or the OFFICIAL SYMBOL can be used) |
mutations |
logical. If TRUE, extended mutation data are fetched instead of the standard TCGA data |
force_numeric |
logical. Shall columns including numeric values be coerced to numeric. |
A data.frame is returned, including the desired TCGA data. Typically, rows are genes and columns are cases. If "extended mutation" data are retrieved (mutations = TRUE), rows correspond to individual mutations while columns are populated with mutation features
Damiano Fantini, damiano.fantini@gmail.com
https://www.data-pulse.com/dev_site/TCGAretriever/
# Mutations occurring on TP53 and PTEN genes in the bladder cancer study
# Returns 1 data frame: rows = genes; columns = cases
x <- fetch_all_tcgadata("blca_tcga_mutations", "blca_tcga_mutations",
c("PTEN", "TP53"), mutation = FALSE)
# Extended mutations occurring on TP53 and PTEN genes in the bladder cancer study
# Returns 1 data frame: rows = mutations; columns = extended information
fetch_all_tcgadata("blca_tcga_all", "blca_tcga_mutations", c("PTEN", "TP53"), mutation = TRUE)