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