narrow and xstringset
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carol white ▴ 680
@carol-white-2174
Last seen 6.3 years ago
European Union
Hi, How can narrow be used with a dnastring? because when i use it with an instance of dnastring I get Error in (function (classes, fdef, mtable)  :   unable to find an inherited method for function ‘narrow’ for signature ‘"DNAString"’ and when i convert the instance of dnastring with DNAStringSet(toString(str)) and use with narrow with any value for end and width I get Error in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord,  :   solving row 1: 'allow.nonnarrowing' is FALSE and the supplied end (500) is > refwidth + 1 Look forward to your reply, carol [[alternative HTML version deleted]]
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@valerie-obenchain-4275
Last seen 22 months ago
United States
Hi, On 08/11/14 06:20, carol white wrote: > Hi, > How can narrow be used with a dnastring? because when i use it with an instance of dnastring I get > > Error in (function (classes, fdef, mtable)? : > ? unable to find an inherited method for function ???narrow??? for signature ???"DNAString"??? That's correct. There is no narrow() method for DNAString. > > > and when i convert the instance of dnastring with > > DNAStringSet(toString(str)) > > > and use with narrow with any value for end and width > > > I get > > Error in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord,? : > ? solving row 1: 'allow.nonnarrowing' is FALSE and the supplied end (500) is > refwidth + 1 > > In your other email on the list (title 'iranges') I explained how 'start' and 'end' work for narrow(). My guess is that was the problem here. d <- DNAString("TTGAAAA-CTC-N") Conversion to string is not necessary, the DNAStringSet can be created with the DNAString. > DNAStringSet(d) A DNAStringSet instance of length 1 width seq [1] 13 TTGAAAA-CTC-N Specify 'start' to begin 3 positions in (greater than) from the current start. > narrow(DNAStringSet(d), 3) A DNAStringSet instance of length 1 width seq [1] 11 GAAAA-CTC-N Valerie > > Look forward to your reply, > > carol > > [[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 > -- Valerie Obenchain Program in Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, Seattle, WA 98109 Email: vobencha at fhcrc.org Phone: (206) 667-3158
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