[Bioc-sig-seq] trimLRPatterns for wild card

[Harris A. Jaffee]

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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