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
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