TCGAcatalogues makes it simple to load mutation catalogues of TCGA cohorts for downstream applications including mutational signature analysis.
Original source of data is the TCGAmutations package, with catalogues generated by sigminer.
You can install the development version of TCGAcatalogues like so:
if (!require("pak", quietly = TRUE))
install.packages("pak")
pak::pak("selkamand/TCGAcatalogues")List available datasets with catalogues_available()
Load datasets with catalogues_load('dataset')
library(TCGAcatalogues)
# List available datasets
catalogues_available()
#> # A tibble: 198 × 4
#> dataset source type genome
#> <chr> <chr> <chr> <chr>
#> 1 ACC MC3 DBS_1248 hg19
#> 2 ACC MC3 DBS_78 hg19
#> 3 ACC MC3 ID_83 hg19
#> 4 ACC MC3 SBS_1536 hg19
#> 5 ACC MC3 SBS_6 hg19
#> 6 ACC MC3 SBS_96 hg19
#> 7 BLCA MC3 DBS_1248 hg19
#> 8 BLCA MC3 DBS_78 hg19
#> 9 BLCA MC3 ID_83 hg19
#> 10 BLCA MC3 SBS_1536 hg19
#> # ℹ 188 more rows# Load datasets
catalogues_collection_acc <- catalogues_load('ACC')
# Load datasets as data.frames
catalogues_dataframe_acc <- catalogues_load('ACC', dataframe = TRUE)If you find TCGAcatalogues useful, please cite both TCGAmutations,
sigminer, and the relevant TCGA study (which you can find by running
maftools::tcgaAvailable())