Question: TCGAbiolinks gives error when parsing a txt file (instead of expected xml)
0
gravatar for andre.verissimo
13 months ago by
andre.verissimo0 wrote:

I was trying to download clinical data from the TCGA-KIRC project and it is failing.

I found out it was downloading a TXT file and trying to read it as an XML (id: 64a1b6e7-d037-4502-bbad-0d07849fc32e and file: nationwidechildrens.org_clinical_nte_kirc.txt

Error:

>   gdc$clinical        <- GDCprepare_clinic(query$clinical, clinical.info = 'patient')
  |==                                                                                                          |   2%Error in doc_parse_file(con, encoding = encoding, as_html = as_html, options = options) : 
  Start tag expected, '<' not found [4]

The code to replicate is below, using bioconductor 3.7 and TCGAbiolinks 2.8.1

project <- 'TCGA-KIRC'
query <- list()
query$clinical <- GDCquery(project = project,
                             data.category = "Clinical")

download.out <- GDCdownload(query$clinical, method = 'api')

gdc <- list()
gdc$clinical        <- GDCprepare_clinic(query$clinical, clinical.info = 'patient')
tcgabiolinks • 494 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by andre.verissimo0

I believe the same question is asked in biostars: https://www.biostars.org/p/320988/

ADD REPLYlink written 13 months ago by andre.verissimo0
Answer: C: TCGAbiolinks gives error when parsing a txt file (instead of expected xml)
2
gravatar for Tiago Chedraoui Silva
13 months ago by
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Tiago Chedraoui Silva240 wrote:

Hello I fixed the documentation yesterday.

It seems the parsed TXT were added to the same group as the XML files.

You need to add file.type = "xml" as filter.

 query <- GDCquery(project = 'TCGA-KIRC', data.category = "Clinical",file.type = "xml")

ADD COMMENTlink written 13 months ago by Tiago Chedraoui Silva240
Thanks for the reply, I've been trying to test confirm to mark this question as resolved, but it continues to say that `GDC server down, try to use this package later`. I will comment back when it allows.
ADD REPLYlink written 13 months ago by andre.verissimo0
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