On 02/22/2010 05:57 AM, Martin Morgan 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)))
To be a little more explicit 'char2phred' needs to be defined to correctly include the encoding (what integer values each letter represents) and what the quality score actually is (Phred above, but `Solexa' quality a possibility); see http://en.wikipedia.org/wiki/FASTQ_format. Martin > 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
