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I ran the following commands:
`query
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Hi,
While running TCGAvisualize_oncoprint() function for visualizing oncoprint, as given in the tutorial at https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.h…
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``` r
query Adding subtype information to samples
Subtype information from:doi:10.1038/nature11252
Error in fix.by(by.y, y): 'by' must specify a uniquely valid column
Traceback:
1. GDCprepare(query)…
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I'm getting an inexplicable error when I try to download data. See code and output below.
``` r
> query GDCdownload(query)
```
trying URL 'https://gdc.nci.nih.gov//files/public/file/gdc-client_v1.0…
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Hi all !
Hope everybody is ok, thanks for the guys who are active here :)
There might a problem with the TCGAdownload function at the moment.
Code that used to work before don't work anymore on my ma…
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Hi.
for several days ago, TCGAquery doesn't work throwing error message as below:
> clinical_brca_data Error in fread(paste0(root, url, "/", files[grep("MANIFEST", files)]), :
> Expected sep ('…
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Hi,
I've encountered with some error when using GDCprepare function.
```
library(TCGAbiolinks)
query = GDCquery(project = 'TCGA-HNSC',
data.category = 'Transcriptome Profiling',
…
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For example, [this](https://gdc-portal.nci.nih.gov/legacy-archive/files/3d23bf42-1761-42b9-b5e1-fa9bbd0b47f0) has everything else but a project, and you can neither query nor download it due to that r…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/ibsquare/MoonlightR
Confirm the following by editing ea…
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While working through some parts of http://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html, I noted some inconsistencies. Fixing them may help others.
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