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waldronlab / cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
https://waldronlab.io/cBioPortalData/
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can't find 'VITAL_STATUS' field in mae clinicalData #34

Closed biodancerwangzhi closed 3 years ago

biodancerwangzhi commented 3 years ago

I tried to use the api to get the clinical data for survial analysis, but I can't get ’OS_MONTHS’, ’VITAL_STATUS’ fields.

clinical_data = clinicalData(cbio, "acc_tcga") clinical_data[,c(’patientId’, ’AJCC_PATHOLOGIC_TUMOR_STAGE’, ’ETHNICITY’, ’OS_MONTHS’, ’VITAL_STATUS’)] I get the error with the official docker image. Thank you for your help.

session info [1] UpSetR_1.4.0 ggplot2_3.3.2 stringr_1.4.0
[4] httr_1.4.2 cBioPortalData_2.1.40 AnVIL_1.1.15
[7] dplyr_1.0.2 MultiAssayExperiment_1.15.4 SummarizedExperiment_1.19.6 [10] DelayedArray_0.15.8 matrixStats_0.56.0 Matrix_1.2-18
[13] Biobase_2.49.1 GenomicRanges_1.41.6 GenomeInfoDb_1.25.11
[16] IRanges_2.23.10 S4Vectors_0.27.13 BiocGenerics_0.35.4
[19] BiocManager_1.30.10

LiNk-NY commented 3 years ago

@biodancerwangzhi

Can you provide more information? I don't see the error. The VITAL_STATUS may not be in the data but there could be other endpoints that provide this data. If so, where do you see this data in the API?

I am using this endpoint: 

cbio <- cBioPortal()
cbio$getAllClinicalDataInStudyUsingGET
LiNk-NY commented 3 years ago

Hi @biodancerwangzhi Please re-open the issue if you have more information to provide. Thank you.