This package contains clinical data from 17 breast cancer studies obtained from cBioPortal:
library(brcaClinical)
brca_clinical[, c('studyId', 'name')]
#> # A tibble: 17 x 2
#> studyId name
#> <chr> <chr>
#> 1 brca_bccrc Breast Invasive Carcinoma (British Columbia, Nature…
#> 2 bfn_duke_nus_2015 Breast Fibroepithelial Tumors (Duke-NUS, Nat Genet …
#> 3 brca_broad Breast Invasive Carcinoma (Broad, Nature 2012)
#> 4 acbc_mskcc_2015 Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pa…
#> 5 brca_igr_2015 Metastatic Breast Cancer (INSERM, PLoS Med 2016)
#> 6 brca_bccrc_xenograft_20… Breast Cancer Xenografts (British Columbia, Nature …
#> 7 breast_msk_2018 Breast Cancer (MSK, Cancer Cell 2018)
#> 8 brca_tcga_pan_can_atlas… Breast Invasive Carcinoma (TCGA, PanCancer Atlas)
#> 9 brca_tcga Breast Invasive Carcinoma (TCGA, Firehose Legacy)
#> 10 brca_mbcproject_wagle_2… The Metastatic Breast Cancer Project (Provisional, …
#> 11 brca_sanger Breast Invasive Carcinoma (Sanger, Nature 2012)
#> 12 breast_alpelisib_2020 Breast Cancer (Alpelisib plus AI, Nature Cancer 202…
#> 13 brca_tcga_pub Breast Invasive Carcinoma (TCGA, Nature 2012)
#> 14 brca_metabric Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2…
#> 15 brca_mskcc_2019 Breast Cancer (MSKCC, NPJ Breast Cancer 2019)
#> 16 brca_tcga_pub2015 Breast Invasive Carcinoma (TCGA, Cell 2015)
#> 17 brca_smc_2018 Breast Cancer (SMC 2018)
The clinical data for each study can be found at the last column of
brca_clinical: clinicalData.
As an example, to have a glimpse at a few selected variables of the clinical data from the METABRIC project:
library(brcaClinical)
metabric_clinical <- brca_clinical$clinicalData$brca_metabric
dplyr::select(metabric_clinical,
patientId,
AGE_AT_DIAGNOSIS,
HISTOLOGICAL_SUBTYPE)
#> # A tibble: 2,509 x 3
#> patientId AGE_AT_DIAGNOSIS HISTOLOGICAL_SUBTYPE
#> <chr> <chr> <chr>
#> 1 MB-0000 75.65 Ductal/NST
#> 2 MB-0002 43.19 Ductal/NST
#> 3 MB-0005 48.87 Ductal/NST
#> 4 MB-0006 47.68 Mixed
#> 5 MB-0008 76.97 Mixed
#> 6 MB-0010 78.77 Ductal/NST
#> 7 MB-0014 56.45 Ductal/NST
#> 8 MB-0020 70.0 Lobular
#> 9 MB-0022 89.08 Mixed
#> 10 MB-0025 76.24 Ductal/NST
#> # … with 2,499 more rows
If you do not have the package remotes install it first:
install.packages("remotes")
Then install brcaClinical:
# Install the package from GitHub
remotes::install_github('maialab/brcaClinical')
Please note that the brcaClinical project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
CC BY-SA 4.0, plus see LICENSE for the licenses of the individual data sets.