brcaClinical

Overview

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)

Usage

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

Installation

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')

Code of Conduct

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.

License

CC BY-SA 4.0, plus see LICENSE for the licenses of the individual data sets.