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 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$strand == -1, left=win[1], right=win[2] ) Error in .bracket.Index(i, lx, asRanges = TRUE) : range index out of bounds Error in as.vector(seqselect(coverage, winCentres[i] + left, winCentres[i] + : error in evaluating the argument 'x' in selecting a method for function 'as.vector' Also you mention endoapply above... it also gave me same error... endoapply(cov.H3K4me1, seqselect, 123456-50, 123456+50) Error in .bracket.Index(i, lx, asRanges = TRUE) : range index out of bounds I found that both of these are exception handling errors but I again I don't know to fix them. It would be great if you can again help on this. Thanks again, Best Regards, Kirti Prakash On Wed, Aug 18, 2010 at 7:33 AM, kirti prakash <[email protected]> wrote: > Hi Martin, > > Thanks a lot for your help. Bioconductor is a great place as one gets > the help from the best and its completely free. Its seems all one > needs to do good research in bioinformatics is a computer, some data > and Bioconductor. > > Its the same tutorial the link you mentioned above . In future I will > attach the pdfs of the tutorials also. > > I did exactly as you told and most the things work fine except... > > Later in the tutorial they use deltaConvolve function... > > H3K4me1 <- deltaConvolve( cov.H3K4me1.chr10, tss, martReply$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 >> > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
