Depending on what you want to do with that file, there may be no need to uncompress …

read.table(), e.g., works fine with the compressed version.

	Benno

On Feb 1, 2012, at 2:04 AM, Luke Miller wrote:

> Try the bzfile() function instead of unz(). You'll find that you're
> taken to the same help page for both of those functions.
> 
> ?bzfile
> 
> On Tue, Jan 31, 2012 at 2:34 PM, ql16717 <ql16717@gmail.com> wrote:
>> 
>> Hi,
>> 
>> I have downloaded a bunch of bz2 files. I wonder if R will be able to
>> unzip them in a batch mode or even one at a time?
>> 
>> I was looking at the unz function. But it didn't work well. Say I have
>> a bz2 file in H:/Temp/65502805_532.pair.bz2. Anyone has any
>> suggestion?
>> 
>> thanks
>> John
>> 
>>> setwd("H:\\Temp\\")
>>> getwd()
>> [1] "H:/Temp"
>>> fn<-list.files(pattern="bz2", full.names=TRUE)
>>> fn
>> [1] "./65502805_532.pair.bz2"
>>> unz(description=fn, filename="65502805_532.pair", open="r")
>> Error in unz(description = fn, filename = "65502805_532.pair", open = "r") :
>>  cannot open the connection
>> In addition: Warning message:
>> In unz(description = fn, filename = "65502805_532.pair", open = "r") :
>>  cannot open zip file './65502805_532.pair.bz2'
>> 
>>> sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>> 
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>> States.1252
>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] pdInfoBuilder_1.18.0 oligo_1.18.1         oligoClasses_1.16.0
>> affxparser_1.26.2    RSQLite_0.10.0
>> [6] DBI_0.2-5            Biobase_2.12.1
>> 
>> loaded via a namespace (and not attached):
>> [1] affyio_1.22.0         Biostrings_2.22.0     bit_1.1-8
>> ff_2.2-4              IRanges_1.12.1
>> [6] preprocessCore_1.16.0 splines_2.14.0        tools_2.14.0
>> zlibbioc_1.0.0
>> 
>> ______________________________________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 

Benno Pütz
Statistical Genetics
MPI of Psychiatry
Kraepelinstr. 2-10
80804 Munich, Germany
T: ++49-(0)89-306 22 222
F: ++49-(0)89-306 22 601




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