Question: Methylation analysis using TCGAbiolinks package
0
gravatar for nazaninhoseinkhan
12 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan400 wrote:

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

methylation tcgabiolinks • 575 views
ADD COMMENTlink modified 10 months ago by zhaoliang03020 • written 12 months ago by nazaninhoseinkhan400

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

ADD REPLYlink written 5 weeks ago by qihengy0
0
gravatar for zhaoliang0302
10 months ago by
zhaoliang03020 wrote:

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

ADD COMMENTlink written 10 months ago by zhaoliang03020

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

ADD REPLYlink written 10 months ago by MatthewP620
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 711 users visited in the last hour