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