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ropensci / UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
https://docs.ropensci.org/UCSCXenaTools
GNU General Public License v3.0
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Cannot query copy number data #7

Closed ShixiangWang closed 5 years ago

ShixiangWang commented 5 years ago

This works in xenaPython

hub = "https://tcga.xenahubs.net" 
dataset = "TCGA.PANCAN.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_by_genes"   
samples = ["TCGA-02-0047-01","TCGA-02-0055-01","TCGA-02-2483-01","TCGA-02-2485-01"] 
In [15]: xena.dataset_fetch(hub, dataset, samples, ["TP53"])                                                                         
Out[15]: [[-0.012, -0.323, -0.033, -0.025]]

In [16]: xena.dataset_probe_values(hub, dataset, samples, ["TP53"])                                                                  
Out[16]: [None, [[-0.012, -0.323, -0.033, -0.025]]]
ShixiangWang commented 5 years ago

This is a mistake :)