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
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
