TCGAbiolinks : Bisulfite-seq data : Legacy archive
1
0
Entering edit mode
DS • 0
@ds-21231
Last seen 5.4 years ago
Belgium

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 bisulfite tcgabiolinks • 1.4k views
ADD COMMENT
1
Entering edit mode
@tiago-chedraoui-silva-8877
Last seen 4.2 years ago
Brazil - University of São Paulo/ Los A…

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 COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 784 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6