i want to remove the PCR2rc from the subject, but it is can not recognized if i set the mismatch =0.2 how can i sent parameter to let trimLRPatterns works GATCGGAAGAGCACACGTCTGAACTCCA TCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG subject<- DNAString(" GATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAA AAAAAAACGACACAAGCCC") PCR2rc <- DNAString("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCT GCTTG") max.mismatchs <- 0.25*1:nchar(PCR2rc) trimLRPatterns( Lpattern = PCR2rc, subject = subject, max.Lmismatch=0.2,with.Rindels=T) 88-letter "DNAString" instance seq: ATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAA AAAAAACGACACAAGCCC trimLRPatterns( Lpattern = PCR2rc, subject = subject, max.Lmismatch=0.5,with.Rindels=T) 27-letter "DNAString" instance seq: AAAAAAAAAAAAAAACGACACAAGCCC countPattern(PCR2rc, subject, max.mismatch= 0.2, min.mismatch=0, with.indels=TRUE) [1] 0 [[alternative HTML version deleted]]

On Oct 11, 2011, at 10:59 AM, wang peter wrote: > i want to remove the PCR2rc from the subject, but it is can not > recognized > if i set the mismatch =0.2 > how can i sent parameter to let trimLRPatterns works > GATCGGAAGAGCACACGTCTGAACTCCA > TCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC > AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG It would really help if you could ask something specific about these 3 strings. > subject<- DNAString(" > GATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAA > AAAAAAACGACACAAGCCC") > PCR2rc <- > DNAString > ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG") Ok, so these are your major players. See below. > max.mismatchs <- 0.25*1:nchar(PCR2rc) I'm ignoring this since it's irrelevant. Now, to get everyone on the same page, let me state some pertinent facts: > PCR2rc.2 <- substr(PCR2rc, 2, nchar(PCR2rc)) > subject 89-letter "DNAString" instance seq: GATCGGAAGAGCACACGTCTGAACTCCATCACATCA...TTCTGCTTGAAAAAAAAAAAAAAACGACACA AG CCC > PCR2rc.2 63-letter "DNAString" instance seq: GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG > neditAt(PCR2rc.2, subject) [1] 32 > neditAt(PCR2rc.2, subject, with.indels=TRUE) [1] 2 So your question is basically how to get a large prefix of the subject trimmed, when it is more like my somewhat artificial 'PCR2rc.2' than your real 'PCR2rc'. > trimLRPatterns( Lpattern = PCR2rc, subject = subject, > max.Lmismatch=0.2,with.Rindels=T) > 88-letter "DNAString" instance > seq: > ATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAA > AAAAAACGACACAAGCCC > > trimLRPatterns( Lpattern = PCR2rc, subject = subject, > max.Lmismatch=0.5,with.Rindels=T) > 27-letter "DNAString" instance > seq: AAAAAAAAAAAAAAACGACACAAGCCC These calls do not make complete sense. You want 'with.*L*indels=TRUE'. More about that later. But doing so, you don't need an absurd max.Lmismatch setting; 0.2 is quite enough: > trimLRPatterns(Lpattern = PCR2rc, subject = subject, max.Lmismatch=0.2, with.Lindels=TRUE) 25-letter "DNAString" instance seq: AAAAAAAAAAAAACGACACAAGCCC > countPattern(PCR2rc, subject, max.mismatch= 0.2, min.mismatch=0, > with.indels=TRUE) > [1] 0 As I've said before, the matchPattern/countPattern family is insensitive to non-integral mismatch values. They are silently truncated, via as.integer(). In this case, your 0.2 becomes 0. Again, the pertinent facts are: > neditAt(PCR2rc, subject, with.indels=TRUE) [1] 3 > countPattern(PCR2rc, subject, max.mismatch=3, with.indels=TRUE) [1] 1 Ok, so now we can consider these somewhat philosophical questions: 1) Should trimLRPatterns save you from setting irrelevant parameters (with.Rindels, when you're "trimming on the left")? 2) Should matchPattern/countPattern save you from a funny mismatch setting? I don't know about 1) per se, but in view of "trimLRPatterns 2.0", the indels parameters will be on/TRUE by default (and possibly not exist at all). For 2), I think you should get a warning, at least, if not a hard error. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor