R help - Aug 2002 - write.table() adds unnecessary spaces to right align integer column

When using write.table() to write data frames the integer columns are padded
with unnecessary spaces (0x20) so that these columns are right align if you
look at them in a text editor. However, I think it is quite a vast of file
size. For instance, I am reading a tab-delimited 4200kb microarray data file
and writing it back verbatim using write.table() and it becomes 5100kb, a
20% increase. Is this problem known and is there anyway to get around it?

Example (R --vanilla):

x <- c(0,1,10,100,1e3,1e5,1e6)
df <- data.frame(a=x, b=as.integer(x), c=as.character(x))
write.table(df, "out.dat")


Output:

"a" "b" "c"
"1" 0e+00       0 "0"
"2" 1e+00       1 "1"
"3" 1e+01      10 "10"
"4" 1e+02     100 "100"
"5" 1e+03    1000 "1000"
"6" 1e+05  100000 "1e+05"
"7" 1e+06 1000000 "1e+06"


str(R.Version()):
 $ platform: chr "i386-pc-mingw32"
 $ arch    : chr "i386"
 $ os      : chr "mingw32"
 $ system  : chr "i386, mingw32"
 $ status  : chr ""
 $ major   : chr "1"
 $ minor   : chr "5.1"
 $ year    : chr "2002"
 $ month   : chr "06"
 $ day     : chr "17"
 $ language: chr "R"

Thanks

Henrik Bengtsson

Dept. of Mathematical Statistics @ Centre for Mathematical Sciences
Lund Institute of Technology/Lund University, Sweden (+2h UTC)
+46 46 2229611 (off), +46 708 909208 (cell), +46 46 2224623 (fax)
h b @ m a t h s . l t h . s e, http://www.maths.lth.se/bioinformatics/

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On Tue, 6 Aug 2002, Henrik Bengtsson wrote:
> When using write.table() to write data frames the integer columns are
padded
> with unnecessary spaces (0x20) so that these columns are right align if you
> look at them in a text editor. However, I think it is quite a vast of file
> size. For instance, I am reading a tab-delimited 4200kb microarray data
file
> and writing it back verbatim using write.table() and it becomes 5100kb, a
> 20% increase. Is this problem known and is there anyway to get around it?
Well, that's not really what write.table is for, so the problem is not with
write.table but with your usage of it.  Is 900kB file space important?  If
so, why are you not using compression?

If you don't want a table for human consumption, use
e.g.save(compress=TRUE).
And if you want to strip blanks in a text file, use an pipe output
connection and strip them with sed, and then compress the file.
> Example (R --vanilla):
>
> x <- c(0,1,10,100,1e3,1e5,1e6)
> df <- data.frame(a=x, b=as.integer(x), c=as.character(x))
> write.table(df, "out.dat")
>
>
> Output:
>
> "a" "b" "c"
> "1" 0e+00       0 "0"
> "2" 1e+00       1 "1"
> "3" 1e+01      10 "10"
> "4" 1e+02     100 "100"
> "5" 1e+03    1000 "1000"
> "6" 1e+05  100000 "1e+05"
> "7" 1e+06 1000000 "1e+06"
>
>
> str(R.Version()):
>  $ platform: chr "i386-pc-mingw32"
>  $ arch    : chr "i386"
>  $ os      : chr "mingw32"
>  $ system  : chr "i386, mingw32"
>  $ status  : chr ""
>  $ major   : chr "1"
>  $ minor   : chr "5.1"
>  $ year    : chr "2002"
>  $ month   : chr "06"
>  $ day     : chr "17"
>  $ language: chr "R"
>
> Thanks
>
> Henrik Bengtsson
>
> Dept. of Mathematical Statistics @ Centre for Mathematical Sciences
> Lund Institute of Technology/Lund University, Sweden (+2h UTC)
> +46 46 2229611 (off), +46 708 909208 (cell), +46 46 2224623 (fax)
> h b @ m a t h s . l t h . s e, http://www.maths.lth.se/bioinformatics/
>
>
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> r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !)  To: r-help-request at
stat.math.ethz.ch
>
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>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
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(in the "body", not the subject !)  To: r-help-request at
stat.math.ethz.ch
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