What is the proper way to replicate the quick select lists seen on the Web UI when using the R cBioPortalData package? I can replicate the TCGA PanCancer by getting all studies and filtering for PanCancer Atlas, but I do not know how to do the same for the non-redundant studies.

Hi Ryan,

There is no "quick select" for the cBioPortalData package, what you can do to find all the studyIds that are from the PanCan Atlas is:

suppressPackageStartupMessages(library(cBioPortalData))
cbio <- cBioPortal()
grep("pan_can", getStudies(cbio)[["studyId"]], value = TRUE)
#>  [1] "acc_tcga_pan_can_atlas_2018"      "blca_tcga_pan_can_atlas_2018"    
#>  [3] "brca_tcga_pan_can_atlas_2018"     "cesc_tcga_pan_can_atlas_2018"    
#>  [5] "coadread_tcga_pan_can_atlas_2018" "chol_tcga_pan_can_atlas_2018"    
#>  [7] "dlbc_tcga_pan_can_atlas_2018"     "esca_tcga_pan_can_atlas_2018"    
#>  [9] "gbm_tcga_pan_can_atlas_2018"      "hnsc_tcga_pan_can_atlas_2018"    
#> [11] "kich_tcga_pan_can_atlas_2018"     "kirc_tcga_pan_can_atlas_2018"    
#> [13] "kirp_tcga_pan_can_atlas_2018"     "laml_tcga_pan_can_atlas_2018"    
#> [15] "lgg_tcga_pan_can_atlas_2018"      "lihc_tcga_pan_can_atlas_2018"    
#> [17] "luad_tcga_pan_can_atlas_2018"     "lusc_tcga_pan_can_atlas_2018"    
#> [19] "meso_tcga_pan_can_atlas_2018"     "ov_tcga_pan_can_atlas_2018"      
#> [21] "paad_tcga_pan_can_atlas_2018"     "pcpg_tcga_pan_can_atlas_2018"    
#> [23] "prad_tcga_pan_can_atlas_2018"     "sarc_tcga_pan_can_atlas_2018"    
#> [25] "skcm_tcga_pan_can_atlas_2018"     "stad_tcga_pan_can_atlas_2018"    
#> [27] "tgct_tcga_pan_can_atlas_2018"     "thca_tcga_pan_can_atlas_2018"    
#> [29] "thym_tcga_pan_can_atlas_2018"     "ucec_tcga_pan_can_atlas_2018"    
#> [31] "ucs_tcga_pan_can_atlas_2018"      "uvm_tcga_pan_can_atlas_2018"

^{Created on 2022-08-22 with [reprex v2.0.2](https://reprex.tidyverse.org)}

You'd have to loop through each study and get the relevant molecularProfileId, etc.

Best,

Marcel