Allowing 2 errors, the first two letters of Rpattern3 match the last
two letters of the subject.
Maybe you want max.Rmismatch=2, which is effectively c(rep(-1,11),2),
or something else to prevent
unintended trimming.
On Oct 9, 2009, at 3:53 PM, joseph wrote:
Hello
In the example below, Rpattern2 (2 mismatches) trims the subject
correctly, while Rpattern3 (3 mismatches) which is not supposed to
do any trimming, it trims the last 2 nucleotides. Can you explain why?
subject <- DNAStringSet("GCTGGAACCCAGGGTGTTGTACCTGTAGGCACCA")
Rpattern2 <- "CTGaAGGCACgA" # 2 mismatches
Rpattern3 <- "tTGaAGGCACgA" # 3 mismatches
trimLRPatterns(Rpattern = Rpattern2, subject = subject,
max.Rmismatch = rep(2, 12))
A DNAStringSet instance of length 1
width seq
[1] 22 GCTGGAACCCAGGGTGTTGTAC
trimLRPatterns(Rpattern = Rpattern3, subject = subject,
max.Rmismatch = rep(2, 12))
A DNAStringSet instance of length 1
width seq
[1] 32 GCTGGAACCCAGGGTGTTGTACCTGTAGGCAC
sessionInfo()
R version 2.10.0 alpha (2009-10-01 r49909)
x86_64-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.5.17 RCurl_1.2-0 bitops_1.0-4.1
ShortRead_1.3.36
[5] lattice_0.17-25 BSgenome_1.13.16 Biostrings_2.13.48
IRanges_1.3.87
loaded via a namespace (and not attached):
[1] Biobase_2.5.8 grid_2.10.0 hwriter_1.1 tools_2.10.0 XML_2.6-0
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