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Reading TCGA methylation .txt files in R

Dear all,

I am trying to analyze Methylation data of cancer patients and compare them with normal samples.

Since the size of methylation data was so huge, I decided to download the entire data as .tar.gz instead of using "GDCdownload" function available in TCGABiolinks.

However I cannot find out how should I read the large number of .txt methylation files after extraction.

Any advice is appreciated

Nazanin

methylation analysis tcga
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written by nazaninhoseinkhan nazaninhoseinkhan

Open a single TXT file and then find out which column(s) that you need to retain. Then, perform the following:

  1. create a vector that contains the path of each TXT file
  2. create a loop that will pass over the contents of the vector
  3. in each loop cycle, read in the desired column(s) and bind these together into a single data-frame
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written by Kevin Blighe Kevin Blighe

Hi Kevin,

Happy new year 2019. Wishing you a prosperous year.

Thank you for your comment.

I will merge the files as you suggest me and let you know the results

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written by nazaninhoseinkhan nazaninhoseinkhan

Hello Nazanin, I know this is an old post but would you be able to share the script you used to accomplish this?

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written by Lemon • Lemon

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