hi all, I'm trying to match 80bp reads to a construct, a sequence of +/- 550bp. The construct contains a strecth of N's, representing a stretch of 20 random nucleotides.
I constructed a pdict from the reads, and a DNAString from the construct. When I run matchPDict with fixed=TRUE, all goes fine and I get 1.2M matches. > construct_mindex <- matchPDict(pdict, DNAString(construct), max.mismatch=3) > sum(countIndex(construct_mindex)) [1] 1280283 With fixed=FALSE I get the following error: > construct_mindex <- matchPDict(pdict, DNAString(construct), max.mismatch=3, > fixed=FALSE) Error in .match.PDict3Parts.XString(pd...@threeparts, subject, max.mismatch, : walk_tb_nonfixed_subject(): implement me Is there a way around this non-implemented function? Or any chance it will be implemented soon? Or am I missing something. If you need more background let me know. Ludo > sessionInfo() R version 2.12.0 Under development (unstable) (2010-06-17 r52313) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.7.7 Rsamtools_1.1.7 lattice_0.18-8 [4] GenomicRanges_1.1.12 Biostrings_2.17.7 IRanges_1.7.7 loaded via a namespace (and not attached): [1] Biobase_2.9.0 grid_2.12.0 hwriter_1.2 tools_2.12.0 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
