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Retrieve TCGA file ID and associated barcode with TCGAbiolinks: "GDC server down"
0
Entering edit mode
14 months ago
user31888 • 60
United States

I am trying to follow the example here to get file names and associated barcodes using TCGAbiolinks.

> library(TCGAbiolinks)
> query <- GDCquery(project = c("TCGA-BRCA"),
              data.category = "Raw Sequencing Data",  
              sample.type = "Primary solid Tumor")
Error in value[[3L]](cond) :
  GDC server down, try to use this package later

I checked the status of the server but apparently it is ok:

> library(GenomicDataCommons)
> status()
$commit
[1] "e9e20d6f97f2bf6dd3b3261e36ead57c56a4c7cc"

$data_release
[1] "Data Release 12.0 - June 13, 2018"

$status
[1] "OK"

$tag
[1] "1.14.1"

$version
[1] 1

Is it possible to similarly get the file names and corresponding barcodes using GenomicDataCommons, which seems to work better?

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3
Entering edit mode
13 months ago
Republic of Ireland

Hello,

Please install the GitHub version by doing the following:

require(devtools)
install_github("BioinformaticsFMRP/TCGAbiolinks")

Then it should work.

query <- GDCquery(project = c("TCGA-BRCA"),
+               data.category = "Raw Sequencing Data",  
+               sample.type = "Primary solid Tumor")
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-BRCA
--------------------
oo Filtering results
--------------------
ooo By sample.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------

Kevin

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0
Entering edit mode

Works ! However, it cannot find function datatable in the second part of the code.

> datatable(getResults(query, rows = 1:100,cols = c("file_name","cases")), 
              filter = 'top',
              options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
              rownames = FALSE)
Error in datatable(getResults(query, rows = 1:100, cols = c("file_name",  :
  could not find function "datatable"
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0
Entering edit mode

My mistake. I just had to get rid of the datatable from the DT package (cannot open browser on the server I use anyway).

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0
Entering edit mode

Great! - all good now?

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