[Bioc-sig-seq] trimLRPatterns question

[Kunbin Qu]

Hi, all:

Is there a way to NOT trim a segment in the pattern from trimLRPatterns? For example:

t1<-DNAString("AAAATGGTAC")
t2<-DNAString("TGGTAC")
t3<-trimLRPatterns(Rpattern=t2, subject=t1, max.Rmismatch = rep(0,4), ranges=T, with.Rindels=TRUE)
t4<-DNAStringSet(t1, start=start(t3), end=end(t3))

> t4
  A DNAStringSet instance of length 1
    width seq
[1]     4 AAAA
> t1
  10-letter "DNAString" instance
seq: AAAATGGTAC
> t2
  6-letter "DNAString" instance
seq: TGGTAC
>


If I want to keep "TG" in t1, followed by the AAAA, which also appears in the beginning of the pattern t2, is there a way? The rep(0,4) does not help since it could find a perfect match at length 6 (the first try when starting to trim). I am trying to use "TG" as my anchor points to avoid false over-trimming. Thanks.

-Kunbin



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