On Jan 19, 2012, at 4:20 PM, Harris A. Jaffee wrote: > To quote from ?trimLRPatterns, for Lpattern here, > > Once the integer vector is constructed using the rules given > above, when 'with.Lindels' is 'FALSE', 'max.Lmismatch[i]' is > the number of acceptable mismatches (errors) between the > suffix 'substring(Lpattern, nLp - i + 1, nLp)' of 'Lpattern' > and the first 'i' letters of 'subject'. When 'with.Lindels' > is 'TRUE', 'max.Lmismatch[i]' represents the allowed "edit > distance" between that suffix of 'Lpattern' and 'subject', > starting at position '1' of 'subject' (as in 'matchPattern' > and 'isMatchingStartingAt'). > > For a given element 's' of the 'subject', the initial segment > (prefix) 'substring(s, 1, j)' of 's' is trimmed if 'j' is the > largest 'i' for which there is an acceptable match, if any. > > If you are asking about implementation, the sub-patterns, i.e suffixes of > Lpattern or prefixes of Rpattern, are tested "longest first" using the > the relevant max.mismatch vector "from the top, down". (Intuitively, you > should think of your max.mismatch vectors as being monotone increasing, > perhaps not strictly.) The testing process at the relevant side of the > subject stops if/when an acceptable match is seen. The See Also refers to > ?`lowlevel-matching`, where you will find which.isMatchingStartingAt() and > which.isMatchingEndingAt(). These functions are called with > auto.reduce.pattern=TRUE, which allows a single "pattern" and single "at" > value to be passed in the context of a *vector* "max.mismatch" value, the > actual pattern being tested getting iteratively shorter by 1 character as > necessary, for each element of the subject, automatically. To clarify, in the C code, there are two loops. There is an outside loop over the subject, and then for each subject element, the specified single pattern is iteratively "auto-reduced" as necessary. > Let me know if I didn't get at your question. > > On Jan 19, 2012, at 3:15 PM, wang peter wrote: > >> hello all: >> >> i want to know how this function process data? >> >> for left match >> it is taken as a "rate" and is converted to >> max.Lmismatch=as.integer(1:nLp *rate ) >> then it try to match between the suffix substring(Lpattern, nLp - i + 1, nLp) >> of Lpattern and the first i letters of subject. >> dees i start from 1 or nLp? and the corresponding allowed mismatch is >> max.Lmismatch[i]? >> >> for the right match >> it is taken as a "rate" and is converted to >> max.Rmismatch=as.integer(1:nRp * rate) >> then it try to match between the suffix substring(Rpattern, nRp - i + 1, nRp) >> of subject and the first i letters of Rpattern. >> dees i start from 1 or nRp? and the corresponding allowed mismatch is >> max.Rmismatch[i]? >> >> -- >> shan gao >> Room 231(Dr.Fei lab) >> Boyce Thompson Institute >> Cornell University >> Tower Road, Ithaca, NY 14853-1801 >> Office phone: 1-607-254-1267(day) >> Official email:sg839 at cornell.edu >> Facebook:http://www.facebook.com/profile.php?id=100001986532253 >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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