Dear all,

I am trying to use TCGAbiolinks to analyze methylation data.

However since I want to analyze only a subset samples (certain tumor stage) of TCGA, I have downloaded those samples and I need to make a change in the following punch of codes to be able to continue methylation analysis:

query.lgg <-GDCquery(project = "TCGA-LGG",
data.category= "DNA methylation",
platform = "Illumina Human Methylation 450",
legacy = TRUE, barcode = lgg.samples)

GDCdownload(query.lgg)

met.lgg <-GDCprepare(query.lgg, save= FALSE)

query.gbm <-GDCquery(project = "TCGA-GBM",
data.category= "DNA methylation",
platform = "Illumina Human Methylation 450",
legacy = TRUE, barcode = gbm.samples)

GDCdownload(query.gbm)

met.gbm <-GDCprepare(query.gbm, save= FALSE)

met <-SummarizedExperiment::cbind(met.lgg, met.gbm)

Can you guide me how should make a change in this code?

Looking forward to your comments

Nazanin