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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
