GEO data retrieve and analyasis

Question

[sainiisha22]

I have download a dataset from GEO i.e in TAR file format. I don't know how to open that data in R.

[Sukhi Singh]

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

Answer 1

[Benn]

Use the function untar in R

Answer 2

[Jenez]

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.

[Benn]

Does that work in R?

[Jenez]

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

[Benn]

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