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
