On 08/17/2010 09:41 PM, kirti prakash wrote: > Hi Martin, > > Thanks a lot for your help. Bioconductor is a great place as one gets > the help from the best and its completely free. Its seems all one > needs to do good research in bioinformatics is a computer, some data > and Bioconductor. > > Its the same tutorial... the link you mentioned above . I cannot > attach the tutorials due to the limit of mail size.
I meant that if the document is available in a public place, then provide a URL to it so that those trying to help can better understand what your problem is. > > I did exactly as you told and most the things work fine except... > > Later in the tutorial they use deltaConvolve function... > > H3K4me1 <- deltaConvolve( cov.H3K4me1.chr10, tss, martReply$strand == > -1, left=win[1], right=win[2] ) > Error in .bracket.Index(i, lx, asRanges = TRUE) : > range index out of bounds > Error in as.vector(seqselect(coverage, winCentres[i] + left, winCentres[i] + > : > error in evaluating the argument 'x' in selecting a method for > function 'as.vector' > > Also you mention endoapply above... it also gave me same error... > > endoapply(cov.H3K4me1, seqselect, 123456-50, 123456+50) > Error in .bracket.Index(i, lx, asRanges = TRUE) : > range index out of bounds One approach to solving problems is to try to simplify them. So let's try to reproduce the error but with a simpler example. You're selecting a subset of an Rle object > seqselect(Rle(1:10, 10:1), 10, 20) 'integer' Rle of length 11 with 3 runs Lengths: 1 9 1 Values : 1 2 3 The error says something about 'index out of bounds', which suggests > seqselect(Rle(1:10, 10:1), 10, 2000) Error in .bracket.Index(i, lx, asRanges = TRUE) : range index out of bounds > seqselect(Rle(1:10, 10:1), -10, 20) Error in .bracket.Index(i, lx, asRanges = TRUE) : range index out of bounds Any hints to what your original problem is, and how to solve it? Martin > > > I found that both of these are exception handling errors but I again I > don't know to fix them. It would be great if you can again help on > this. > > Thanks again, > > Best Regards, > > Kirti Prakash > > On Wed, Aug 18, 2010 at 7:33 AM, kirti prakash > <[email protected]> wrote: >> Hi Martin, >> >> Thanks a lot for your help. Bioconductor is a great place as one gets >> the help from the best and its completely free. Its seems all one >> needs to do good research in bioinformatics is a computer, some data >> and Bioconductor. >> >> Its the same tutorial the link you mentioned above . In future I will >> attach the pdfs of the tutorials also. >> >> I did exactly as you told and most the things work fine except... >> >> Later in the tutorial they use deltaConvolve function... >> >> H3K4me1 <- deltaConvolve( cov.H3K4me1.chr10, tss, martReply$strand == >> -1, left=win[1], right=win[2] ) >> Error in .bracket.Index(i, lx, asRanges = TRUE) : >> range index out of bounds >> Error in as.vector(seqselect(coverage, winCentres[i] + left, winCentres[i] + >> : >> error in evaluating the argument 'x' in selecting a method for >> function 'as.vector' >> >> Also you mention endoapply above... it also gave me same error... >> >> endoapply(cov.H3K4me1, seqselect, 123456-50, 123456+50) >> Error in .bracket.Index(i, lx, asRanges = TRUE) : >> range index out of bounds >> >> >> I found that both of these are exception handling errors but I again I >> don't know to fix them. It would be great if you can again help on >> this. >> >> Thanks again, >> >> Best Regards, >> >> Kirti Prakash >> >> >> >> >> On Tue, Aug 17, 2010 at 7:47 PM, Martin Morgan <[email protected]> wrote: >>> kirti prakash <[email protected]> writes: >>> >>>> Hi, >>>> >>>> I was reading the material "EMBL course on Short Read analysis with >>>> Bioconductor: An exercise with coverage vectors" by Simon Anders. >>> >>> It took me a second to find >>> >>> >>> http://bioconductor.org/help/course-materials/2009/EMBLJune09/Practicals/TSS/ >>> >>> is that the tutorial you mean? >>> >>>> >>>> I tried this... >>>> aln <- readAligned("dirPath", pattern="sequence.map", type="Bowtie") >>>> cov = coverage(aln) >>>> cov >>>> [[1]] >>>> SimpleRleList of length 25 >>>> $chr1 >>>> 'integer' Rle of length 247188620 with 840106 runs >>>> Lengths: 463 36 6823 36 550058 ... 713 36 2034 >>>> 36 >>>> Values : 0 1 0 1 0 ... 0 1 0 >>>> 2 >>>> >>>> $chr10 >>>> 'integer' Rle of length 135373320 with 446681 runs >>>> Lengths: 88078 36 3880 36 12451 ... 20 50 36 22054 36 >>>> Values : 0 1 0 1 0 ... 1 0 1 0 1 >>>> . >>>> . >>>> . >>>> >>>>> cvg <- cov$chr10 >>>>> as.vector(subseq(cvg, 123456+50, 123456-50)) >>> >>> I think this should be >>> >>> seqselect(cvg$chr10, 123456+50, 123456-50) >>> >>> or, to subset all chromosomes, >>> >>> endoapply(cvg, seqselect, 123456+50, 123456-50) >>> >>> (though it doesn't seem like you'd usually want to select consistent >>> coordinates across chromosomes). >>> >>> To get here, I looked up the help page for Rle-class >>> >>> > class?Rle >>> >>> This is with >>> >>>> sessionInfo() >>> R version 2.11.1 Patched (2010-06-03 r52215) >>> x86_64-unknown-linux-gnu >>> >>> 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_1.6.2 Rsamtools_1.0.5 lattice_0.18-8 >>> [4] Biostrings_2.16.9 GenomicRanges_1.0.5 IRanges_1.6.11 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.8.0 grid_2.11.1 hwriter_1.2 tools_2.11.1 >>> >>> Martin >>> >>> >>>> Error in function (classes, fdef, mtable) : >>>> unable to find an inherited method for function "subseq", for signature >>>> "list" >>>> Error in as.vector(subseq(cvg, 123456 + 50, 123456 - 50)) : >>>> error in evaluating the argument 'x' in selecting a method for >>>> function 'as.vector' >>>> >>>> I guess * 'integer' Rle of length* should be 'numeric' Rle of length >>>> as per the booklet ... but I don't know how to fix it. >>>> >>>> I know I am making some stupid mistake. It would be great if anyone >>>> can provide some help on this. >>>> >>>> Thank you, >>>> >>>> Best regards, >>>> >>>> Kirti Prakash >>>> >>>> _______________________________________________ >>>> Bioc-sig-sequencing mailing list >>>> [email protected] >>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >>> -- >>> Martin Morgan >>> 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 >>> >> -- Martin Morgan 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
