[Bioc-sig-seq] apply/sapply for DNAStringSet class or FastqQuality class?

[Martin Morgan]

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
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