Sorry, I'll get it eventually. answer = which.isMatchingAt("N", seqs, at=6:1, follow.index=TRUE) Let me know if anything beats it. On Jan 19, 2012, at 6:15 PM, Harris A. Jaffee wrote: > Or maybe > > n = narrow(seqs, 1, 6) > answer = 6 - nchar(sub(".*N", "", n)) > > On Jan 19, 2012, at 6:01 PM, Harris A. Jaffee wrote: >> Perhaps something along the lines >> >> r = reverse(narrow(seqs, 1, 6)) >> answer = 7 - which.isMatchingAt("N", r, at=1:6) >> >> On Jan 19, 2012, at 5:26 PM, wang peter wrote: >>> i have some reads from illumina sequencer >>> there are some "N" in the reads >>> i want to find the last "N" in the first 6 bp of the sequence >>> so do you think matchPattern is faster ? or other low-level match >>> methods? >>> >>> reads <- readFastq(fastqfile) >>> seqs <- sread(reads); >>> matchPattern("N", seqs) >>> >>> >>> >>> -- >>> shan gao >>> Room 231(Dr.Fei lab) >>> Boyce Thompson Institute >>> Cornell University >>> Tower Road, Ithaca, NY 14853-1801 >>> Office phone: 1-607-254-1267(day) >>> Official email:sg839 at cornell.edu >>> Facebook:http://www.facebook.com/profile.php?id=100001986532253 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/ >>> gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor