Harris, another question following your advice. If I have a case like the following:
fixedPattern1_NNNNN_fixedPattern1 would the Rfixed help me, as the NNNNN is not at the right end? Or should I consider using with.Lindel and withRindel? Thanks. -Kunbin -----Original Message----- From: Harris A. Jaffee [mailto:[email protected]] Sent: Thursday, September 23, 2010 11:56 AM To: Kunbin Qu Cc: [email protected] Subject: Re: [Bioc-sig-seq] trimLRPatterns for wild card Let me try again. You want Rfixed="subject", only. Rfixed=FALSE works in your case by accident since your subject does not contain N. If it did, the N's would match anything in your pattern, which isn't what you want. To clean up another issue, with Rfixed=FALSE, one would expect that both the pattern and subject would have to be DNA or RNA, and that is eventually correct. But, by the time it matters, if your subject is one of those types, your pattern will have been converted accordingly for you, automatically. On Sep 23, 2010, at 2:01 PM, Harris A. Jaffee wrote: > You need to set 'Rfixed' to either FALSE or "subject": > > trimLRPatterns(Rpattern=p, subject=a, Rfixed=FALSE) > > trimLRPatterns(Rpattern=p, subject=a, Rfixed="subject") > > See ?matchPattern and ?`lowlevel-matching`. > > By the way, your pattern did not have to be a DNAString. "CCNNT" > would have been fine. But the ambiguity machinery with regard to > the subject requires that it be an RNA- or DNAString. > > -Harris > > On Sep 23, 2010, at 1:32 PM, Kunbin Qu wrote: > >> Hi, all, >> >> Does trimLRPatterns function take wild card N? When I tested it, >> it does not seem to work. Is there a way to do that? Thanks. >> >> -Kunbin >> >> >>> a<-DNAString("AAACCCCTTTCCTTT") >>> p<-DNAString("CCNNT") >>> trimLRPatterns(Rpattern=p, subject=a) >> 15-letter "DNAString" instance >> seq: AAACCCCTTTCCTTT >>> p<-DNAString("CCTTT") >>> trimLRPatterns(Rpattern=p, subject=a) >> 10-letter "DNAString" instance >> seq: AAACCCCTTT >>> >> >> _____________________________________________________________________ >> _ >> The contents of this electronic message, including any >> attachments, are intended only for the use of the individual or >> entity to which they are addressed and may contain confidential >> information. If you are not the intended recipient, you are hereby >> notified that any use, dissemination, distribution, or copying of >> this message or any attachment is strictly prohibited. If you have >> received this transmission in error, please send an e-mail to >> [email protected] and delete this message, along with >> any attachments, from your computer. >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > ______________________________________________________________________ The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to [email protected] and delete this message, along with any attachments, from your computer. _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
