Hi Marcus, Actually, I originally tried using the method (if it existed) to update the ids but got the error that you show above. By the way, going through my records I found that indeed I had a typo. I meant to write ShortReadQ() but I wrote ShortRead(). No wonder it complained about not having a slot for quality. Thank you, Ivan Ivan Gregoretti, PhD Bioinformatics On Mon, Oct 7, 2013 at 11:24 PM, Marcus Davy <mdavy86 at="" gmail.com=""> wrote: > It doesn't look like a method has been written to update the id slot, direct > access does work, I also think using renew() is nicer. > > try(id(srq1) <- paste(id(srq1), 'tested')) > Error in id(srq1) <- paste(id(srq1), "tested") : > could not find function "id<-" > > ## Direct injection -probably not recommended > srq1 at id <- BStringSet( paste(id(srq1), 'tested')) > > renew() also catches enforced structure between 'sread' and 'quality', e.g. > > try(renew(srq1, quality=FastqQuality(c("HH","H")))) > Error in validObject(.Object) : > invalid class "ShortReadQ" object: some sread and quality widths differ > > I have also had cause to update ids in a ShortReadQ object, in my case for > input into a Short read aligner, useful additional auxiliary information can > go into the QNAME field of a bam file. > > cheers, > > Marcus > > > > > On Tue, Oct 8, 2013 at 1:44 PM, Ivan Gregoretti <ivangreg at="" gmail.com=""> wrote: >> >> The renew() looks really handy. The direct use of the constructor is >> something that I tried but failed to me. I probably had one of those >> invisible typos. >> >> Thank you. >> >> Ivan >> >> >> Ivan Gregoretti, PhD >> Bioinformatics >> Cell Signaling Technology, Inc >> 3 Trask Lane >> Danvers, MA 01923. USA. >> Phone +1-978-867-2429 >> >> >> On Mon, Oct 7, 2013 at 8:31 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> > On 10/07/2013 05:06 PM, Ivan Gregoretti wrote: >> >> >> >> Hello Martin, >> >> >> >> Great. So, >> >> >> >> srq1 <- ShortReadQ(DNAStringSet(c("ACGT", "GGGGACT")), >> >> FastqQuality(c("HHHH", "HHHHHHH")), BStringSet(c("read1", "read2"))) >> >> >> >> gets me what I wanted. Now I have a part two to my question: >> >> >> >> How do I modify srq1's id? >> >> >> >> For instance, id(srq1) produces >> >> >> >>> id(srq1) >> >> >> >> A BStringSet instance of length 2 >> >> width seq >> >> [1] 5 read1 >> >> [2] 5 read2 >> >> >> >> but I want to modify srq1's id so that it looks like this >> >> >> >>> BStringSet(paste(id(srq1), 'tested')) >> >> >> >> A BStringSet instance of length 2 >> >> width seq >> >> [1] 12 read1 tested >> >> [2] 12 read2 tested >> >> >> >> Please note that I intend not to construct a new instance by passing >> >> FastqQuality(c("HHHH", "HHHHHHH")) and DNAStringSet(c("ACGT", >> >> "GGGGACT")). I intend to copy srq1 to srq2 and then modify srq2. >> >> >> > >> > ShortRead explored the notion of a 'renw'able instance, see ?renew and >> > >> > srq2 = renew(srq1, id=BStringSet(paste(id(srq1), "tested"))) >> > >> > this >> > >> > ShortReadQ(sread(srq1), quality(srq1), BStringSet(paste(id(srq1), >> > "tested"))) >> > >> > also works >> > >> > Martin >> > >> > >> >> Alternatively, may I construct a new instance by passing >> >> BStringSet(paste(id(srq1), 'tested')), sread(srq1) and quality(srq1)? >> >> I tried by the constructor complained vociferously when I passed >> >> quality=quality(srq1). >> >> >> >> Thank you, >> >> >> >> Ivan >> >> >> >> >> >> >> >> >> >> Ivan Gregoretti, PhD >> >> Bioinformatics >> >> >> >> >> >> >> >> >> >> On Mon, Oct 7, 2013 at 3:44 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> >> >> wrote: >> >>> >> >>> On 10/07/2013 12:28 PM, Ivan Gregoretti wrote: >> >>>> >> >>>> >> >>>> Hello, >> >>>> >> >>>> Could somebody show an example of constructing a ShortReadQ object >> >>>> instance? I can't find an example in the documentation. >> >>>> >> >>>> >> >>>> For example, lets say that I have two records with the following ids, >> >>>> sequences, and Phred qualities >> >>>> >> >>>> c("read1", "read2") >> >>>> c("ACGT", "GGGGACT") >> >>>> c("HHHH", "HHHHHHH") >> >>>> >> >>>> How would you now construct the ShortReadQ instance? >> >>> >> >>> >> >>> >> >>> Hi Ivan >> >>> >> >>> ShortReadQ(DNAStringSet(c("ACGT", "GGGGACT")), >> >>> FastqQuality(c("HHHH", "HHHHHHH")), >> >>> BStringSet(c("read1", "read2"))) >> >>> >> >>> Martin >> >>> >> >>>> >> >>>> Thank you, >> >>>> >> >>>> Ivan >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> Ivan Gregoretti, PhD >> >>>> Bioinformatics >> >>>> >> >>>> _______________________________________________ >> >>>> 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 >> >>>> >> >>> >> >>> >> >>> -- >> >>> Computational Biology / Fred Hutchinson Cancer Research Center >> >>> 1100 Fairview Ave. N. >> >>> PO Box 19024 Seattle, WA 98109 >> >>> >> >>> Location: Arnold Building M1 B861 >> >>> Phone: (206) 667-2793 >> > >> > >> > >> > -- >> > Computational Biology / Fred Hutchinson Cancer Research Center >> > 1100 Fairview Ave. N. >> > PO Box 19024 Seattle, WA 98109 >> > >> > Location: Arnold Building M1 B861 >> > Phone: (206) 667-2793 >> >> _______________________________________________ >> 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 > >