thanks!

On Mon, Feb 22, 2010 at 2:57 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 02/22/2010 02:36 AM, Johannes Rainer wrote:
> > hi,
> >
> > I'm just wondering of there is a "apply" function for the classes defined
> in
> > the ShortRead package.
> > Or is there a nice and fast way to e.g. calculate the mean Phred quality
> for
> > each aligned sequence? note, I can not use the as( quality( AlignedReads
> ),
> > "matrix" ), because the lengths of the alignments (i.e. aligned
> sequences)
> > differs in my data set.
>
> An approximate way is ?alphabetScore, which calculates the sum of the
> _encodings_ (not quite quality scores) of each read. Another way is
>
>  char2phred <- function(p) -10*log10(as.integer(charToRaw(p)))
>  phred = lapply(as.character(quality(quality(aln))), char2phred)
>
> One might also try
>
>  lapply(quality(quality(aln)), char2phred)
>
> which is more memory efficient but slow.
>
> Martin
>
> >
> > thanks!
> >
> > cheers, jo
> >
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
Johannes Rainer, PhD
Bioinformatics Group,
Division Molecular Pathophysiology,
Biocenter, Medical University Innsbruck,
Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria
and
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria

Tel.:     +43 512 570485 13
Email:  johannes.rainer@i-med.ac.at
           johannes.rainer@tcri.at
URL:   http://bioinfo.i-med.ac.at

	[[alternative HTML version deleted]]

