RTCGAToolbox and miRNA-seq data - no download.
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@federicocomoglio-4524
Last seen 4.4 years ago
Switzerland

In a recent project, I used the BioC package RTCGAToolbox to conveniently fetch data from TCGA. 

I now would like to download miRNA expression data for the TCGA AML patient cohort. However, while I can successfully download all other data types, miRNA expression profiles are not retrieved.

A call to (tested with any runDate)

getFirehoseData(dataset = 'LAML', runDate = '20160128', forceDownload = TRUE, miRNASeq_Gene = TRUE, miRNA_Array = TRUE) 

fetches only the clinical data. In contrast, setting other arguments to TRUE (e.g. RNAseq2_Gene_Norm = TRUE or Mutation = TRUE) works very well. Neither fileSizeLimit nor the project date are an issue here - I tried several.

One thing I noticed in the getFirehoseData function is that the internal function .getLinks is called with different arguments if RNAseq2_Gene_Norm=TRUE or if miRNASeq_Gene=TRUE. Not sure how relevant this is, though.

I contacted the developer but I didn't get an reply, yet. Thank you very much for your help.

F

 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.3 (Sierra)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RTCGAToolbox_2.2.2

loaded via a namespace (and not attached):
 [1] RCircos_1.1.3    Matrix_1.2-7.1   limma_3.28.21    formatR_1.4      tools_3.3.1     
 [6] RCurl_1.95-4.8   survival_2.40-1  RJSONIO_1.3-0    splines_3.3.1    grid_3.3.1      
[11] data.table_1.9.6 knitr_1.14       chron_2.3-47     bitops_1.0-6     lattice_0.20-34 
[16] XML_3.98-1.4    
RTCGAToolbox • 540 views
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Anyone knows how to go about this?

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