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Why "Parse XML clinical data" in TCGAbiolinks gives error in Rstudio ?

The following command for TCGA - clinical data gives error in TCGAbiolinks. I am trying to parse XML clinical data

query <- GDCquery(project = "TCGA-PRAD", 
              data.category = "Clinical")


radiation<-GDCprepare_clinic(query, clinical.info = "radiation")

|==== | 4% Error in doc_parse_file(con, encoding = encoding, as_html = as_html, options = options) : Start tag expected, '<' not found [4]

I assume it is because of big file size. How can I solve the problem ?

tcgabiolinks xml clinical data
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updated by afsverissimo • afsverissimo • written by Björn • Björn

tag expected, '<' not found [4]

it's because it's not a xml file, or the file is corrupted.

test this with:

xmllint --stream --noout your.xml
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks,I have nearly 600 individual xml files in individual folders which is standard download from TCGA. So, no idea how to sort it out?

• 1 views • link
written by Björn • Björn 
find /path/to/dir  -type f -name "*.xml" -exec xmllint --stream --noout '{}' ';'
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

facing the same problem, all of them are valid xml

edit: for KIRC project instead, something weird as there should be 627 patients, but only 621 xml files in clinical directory

edit2: all files in results from query exist, so there are multiple references for same file

• 1 views • link
written by afsverissimo • afsverissimo

actually, the code is trying to read a txt file as xml -_-

I'm guessing this is a problem with tcgabiolinks trying to parse wrong files or not recognizing that it is not a xml

find /path/to/dir -type f -name "*.txt"

• 1 views • link
written by afsverissimo • afsverissimo

1 answer

According to Bioconductor support website, you need to filter out xml files

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

Here is the link: https://support.bioconductor.org/p/110056/#110057

I haven't been able to confirm this as TCGAbiolinks is saying that GDC server is down.

edit: solution works for me. I solved the last problem by using the github version of the package

• 1 views • link
written by afsverissimo • afsverissimo

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