R-API Quick Select?
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@cd1dac3b
Last seen 5 months ago
United States

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.

cBioPortalData • 352 views
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@marcel-ramos-7325
Last seen 2 days ago
United States

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

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That did not address my question fully. There are two "quick select" buttons on the cBioPortal landing page. I mentioned in my question that I could already do precisely what your code does to replicate the "TCGA PanCancer Atlas Studies" button. Is there a way to replicate the other button for "Curated set of non-redundant studies" using the cBioPortalData package?

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Hi Ryan,

Thanks for clarifying. I initially did not understand your question.

These Quick Select buttons on the website are lists of studies. I am not sure if they're available anywhere.

I have asked the cBioPortal team for more information.

Currently there is no parallel operation in the package for these operations.

Best regards,

Marcel

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The cBioPortal team member said that they will make the lists available via the API and have filed an issue.

For now, you can find the list here:

https://github.com/knowledgesystems/knowledgesystems-k8s-deployment/blob/master/cbioportal/cbioportal_spring_boot.yaml#L86

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Excellent! I knew the list had to be somewhere already so thank you for linking it. This works perfectly for my needs right now. I am glad to hear an issue has been filed as well.

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