[R] Pack and Unpack Strings in R

[Martin Morgan]

Gundala --

Gundala Viswanath wrote:
> Dear all,
> 
> Does R has any function/package that can pack
> and unpack string into bit size?

All of your questions relate to DNA strings. The R/Bioconductor package 
Biostrings is designed to manipulate such objects. It does not 
necessarily address this particular problem (because in general DNA 
strings contain any of the 16 IUPAC symbols and hence compression 
becomes less compelling, and as you indicate even with compression the 
size of the data means that one might often need to process parts of the 
data at a time), but may provide useful containers and methods that make 
such issues less important.

 > source('http://bioconductor.org/biocLite.R')
 > biocLite('Biostrings')
 > library('Biostrings')

see also the vignettes for the package, available within R or for example at

http://bioconductor.org/packages/release/bioc/html/Biostrings.html

It seems that you have data suitable for representation as a DNAStringSet.

The package is actively developed, and using the 'devel' version of R 
(and hence 'devel' version of Biostrings) might provide additional 
important facilities. If this proves useful then follow-up questions 
should use the Bioconductor mailing lists

http://bioconductor.org/docs/mailList.html

Martin

> The reason I want to do this in R is that R
> has much more native statistical function than Perl.
> 
> Yet the data I need to process is so large that it
> required me to compress it into smaller unit -> process it -> finally
> recover them back again into string with new information.
> 
> In Perl the implementation will look like this:
> I wonder how can this be implemented in R.
> 
> __BEGIN__
> my %charmap = (
>     A => '00',
>     C => '01',
>     G => '10',
>     T => '11',
> );
> 
> my %digmap = (
>     '00'    => "A",
>     '01'    => "C",
>     '10'    => "G",
>     '11'    => "T",
> );
> 
> my $string = 'GATTA';
> $string =~ s/(.)/$charmap{$1}/ge;
> 
> my $compressed = pack 'b*', $string;
> 
> print "COMP: $compressed\n";
> printf "%d bytes\n", length $compressed;
> 
> my @data;
> 
> # Store the compressed bit into array
> push @data, $compressed;
> 
> # process the array
> foreach my $dat ( @data ) {
> 
>    my $decompressed = unpack 'b*', $dat;
>    $decompressed =~ s/(..)/$digmap{$1}/ge;
> 
>    print "$decompressed\n";
>    # or do further processing on $dat
> }
> __END__
> 
> 
> - Gundala Viswanath
> Jakarta - Indonesia
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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