Question: GEO data retrieve and analyasis
0
gravatar for sainiisha22
3.2 years ago by
sainiisha220 wrote:

i have download a dataset from GEO  i.e in TAR file format.. i dont know how to open that data in R.

 

R • 991 views
ADD COMMENTlink modified 3.2 years ago by Jenez520 • written 3.2 years ago by sainiisha220

GEO is a big data archive, depending on what kind of file you have downloaded, its better to pre-process (extract/sanity check) on command line and then proceed to R. If you are doing it routinely, better is check SRAdb pakage.

Using the SRAdb Package to Query the Sequence Read Archive

ADD REPLYlink written 3.2 years ago by Sukhdeep Singh9.7k
0
gravatar for Benn
3.2 years ago by
Benn6.6k
Netherlands
Benn6.6k wrote:

Use the function untar in R

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Benn6.6k
0
gravatar for Jenez
3.2 years ago by
Jenez520
Sweden
Jenez520 wrote:

Extract the contents of the tar file first?

tar -xzf "filename.tar.gz"

And this is not a bioinformatical question. A simple google search of 'tar files' would've explained it.

ADD COMMENTlink modified 3.2 years ago by Sukhdeep Singh9.7k • written 3.2 years ago by Jenez520

Does that work in R?

ADD REPLYlink written 3.2 years ago by Benn6.6k

It's bash command line. I was questioning why not just extract the .tar before attempting to process it

ADD REPLYlink written 3.2 years ago by Jenez520

I know, but the question was how to open in R right?

ADD REPLYlink written 3.2 years ago by Benn6.6k
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