Question: TCGAbiolinks : Bisulfite-seq data : Legacy archive
0
gravatar for DS
4 months ago by
DS0
Belgium
DS0 wrote:

Hello,

I am trying to use TCGAbiolinks to query GDC for Bisulfite-seq data. It is part of the "Legacy archive".

> library(TCGAbiolinks)
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
> query <- GDCquery(project = c("TCGA-COAD"),
+                   data.category = "DNA methylation",
+                   legacy = TRUE,
+                   platform = c("IlluminaHiSeq_WGBS"),
+                   sample.type = "Recurrent Solid Tumor"
+ )
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-COAD
--------------------
oo Filtering results
--------------------
Error in GDCquery(project = c("TCGA-COAD"), data.category = "DNA methylation",  : 
  Please set a valid platform argument from the list below:
  => Illumina Human Methylation 450

Though IlluminaHiSeq_WGBS is mentioned as an argument for platform in https://www.bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/query.html, and Bisulfire-seq data is available for TCGA-COAD in the GDC Legacy archive, why am I not able to query it through TCGAbiolinks ?

Thank you

tcga tcgabiolinks bisulfite • 96 views
ADD COMMENTlink modified 4 months ago by Tiago Chedraoui Silva240 • written 4 months ago by DS0
Answer: TCGAbiolinks : Bisulfite-seq data : Legacy archive
1
gravatar for Tiago Chedraoui Silva
4 months ago by
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Tiago Chedraoui Silva240 wrote:

The correct code to access WGBS would be:

query <- GDCquery(project = c("TCGA-COAD"),
                  legacy = TRUE,
                  data.category = "DNA methylation",
                  data.type = "Methylation percentage",
                  experimental.strategy = "Bisulfite-Seq")

However there is no Recurrent Solid Tumor for COAD WGBS.

However, there is no Recurrent Solid Tumor for COAD WGBS.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Tiago Chedraoui Silva240

Thank you for helping me out ! I am able to query for WGBS now.

ADD REPLYlink written 4 months ago by DS0
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