Methylation analysis using TCGAbiolinks package

Question

[nazaninhoseinkhan]

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

[qihengy]

Hey there! Have you figured it out? I am really interested in this question as well!

Answer 1

[zhaoliang0302]

By the way, do you know how to define a gene is methlated or not? Such as MGMT in glioma, many papers didn't provide the method. I downloaded the methylation data and i don't know how to decide methylation according to the beta value. Thanks, Zhao

[MatthewP]

You are not providing answer don't post here. Post a new question is better.