Both pairs of R/L- arguments refer to a "context" in the subject.
Nothing refers to where N's might be in your pattern. Whether you
want to allow indels in the matching is a different story, and it's
your decision, maybe depending on the number of N's in your _NNNNN_
and the rest of your whole situation.
If I understand the question, this is a good example from ?
matchPattern :
## A simple inexact matching example with a short subject:
x <- DNAString("AAGCGCGATATG")
m1 <- matchPattern("GCNNNAT", x)
m1
m2 <- matchPattern("GCNNNAT", x, fixed=FALSE)
m2
Except, again, fixed="subject" is probably better.
On Sep 23, 2010, at 3:08 PM, Kunbin Qu wrote:
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
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