[R] how to read/save .zip compressed files from R?

[J.delasHeras at ed.ac.uk]

Quoting Jeff Newmiller <jdnewmil at dcn.davis.ca.us>:

> In the way you describe it, no.
>
> A) There is no such thing as a "zip folder". You are most likely   
> being fooled by the visual presentation of zip files in Windows   
> Explorer, which automatically simulates it as a  folder, when it is   
> really extracting bits of data as needed to display it.
>
> B) Because the data must be decompressed to be manipulated, there is  
>  no performance or disk space advantage to creating a facility such   
> as you describe, though thee may be a convenience factor if you do   
> it a lot.


I will be doing a lot, that's why I wanted to automate it and since I  
can use R I was wondering.

I'm using a software for displaying protein interactions as a network  
of configurable nodes and edges. I have created my interaction maps  
and attributes etc using R, then using the software for visualisation.  
It allows me to see the network, colour-coded, and I can display all  
sorts of interesting parameters of my choice. The software saves the  
session in what seems to be nothing but a .zip file under a made up  
extension name.
I can send these "all-encompassing" files to my collaborators and they  
can see the networks I have created, and further filter and explore  
using some simple menus the software provides.

The software has a small bug affecting the order of the annotation  
columns it displays, and I tracked it down to one of the files it  
saves within the .zip. I can alter the file so that the session opens  
as I intend. It's a simple change to make. But I need to do it with  
every file everytime I alter something and save it.

I do not have the ability to fix the bug itself, so until then I  
figured it'd be good to have a little script that I can run to do that  
for me.


> C) There is a function zip.file.extract() in R for extraction, but I  
>  don't see a zip compression function, so you will need to use   
> external programs, perhaps executed using the "system" function, to   
> generate updated zip files.

thank you, I will check that.

Jose


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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6507095
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