Question: (Closed) unpacking zipped file in R
0
gravatar for Angel
4.2 years ago by
Angel3.5k
Angel3.5k wrote:

hello,

i have 96 arrays in a zipped file, i did so to unpacking but recieved error, what happened please?

i changed directory and typed:

> untar("GSE63706_RAW.tar", exdir="data")
> cels = list.files("data/", pattern = "CEL")
> sapply(paste("data", cels, sep="/"), gunzip)
Error in match.fun(FUN) : object 'gunzip' not found
>

R software error • 3.0k views
ADD COMMENTlink modified 4.2 years ago by Giovanni M Dall'Olio26k • written 4.2 years ago by Angel3.5k
2

Hello sarah!

We believe that this post does not fit the main topic of this site.

not a bioinformatics question, see the documentation https://stat.ethz.ch/R-manual/R-devel/library/utils/html/unzip.html

or http://stackoverflow.com/questions/5764499/decompress-gz-file-using-r

Before you open another thread here elsewhere please learn to google.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Michael Dondrup46k
1

I would propose you a different approach to get the data.

Use the GEOquery package from bioconductor to download the data directly from R:

source("http://bioconductor.org/biocLite.R")
biocLite("GEOquery")
library("GEOquery")
GSE63706 = getGEO("GSE63706")

Check the GEOquery vignette for more information on how to access the data. Check also the destdir option of getGEO for saving the downloaded file to your preferred folder.

By the way, regarding your original question: you usually don't need to uncompress files because R is usually faster at reading compressed files than uncompressed (depending on your disk read speed and ram access time).

ADD REPLYlink written 4.2 years ago by Giovanni M Dall'Olio26k

thank you Giovanni

ADD REPLYlink written 4.2 years ago by Angel3.5k
1

Hello,

Actually, this problem presented above by Fereshteh,it is part of a tutorial to perform microarray data analyses using a dataset from GEO- NCBI db.https://www.biostars.org/p/53870/ .

I have similar problem and been trying to resolve it. I first tried using getGeo to download datasets in GSE matrix format, which is easy to analyse further in R but the challenge is that i have encountered incomplete downloads interuppting my pipeline, so i decided to use raw data format getGEOsuppFiles().

Has anyone resolved this problem? can anyone help please? thanks in advance

---------------------------------------------------

R sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  base     

 

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by i.eberechi10

I would just use 7zip :)

http://www.7-zip.org/

ADD REPLYlink written 4.2 years ago by roy.granit800

no i don't think it could unpack all to CEL files

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Angel3.5k
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