Hi Patrick Trying few more things I was atleast able to deal with selecting only one Chr with filtered reads.
ned_chr <- chromosome(aln) == "K-10_OM_revised.fasta" filtered <- alignData(aln)[["filtering"]] == "Y" aln_chr_1_filt <- aln[ned_chr & filtered] levels(chromosome(aln_chr_1_filt) ) [1] "K-10_OM_revised.fasta" But the problem with coverage functions still remains the same. cov_rLe <- coverage(x=aln_chr_1_filt, start=1, end=4832581, shift=0L, width=NULL,weight=1L,coords="leftmost",extend=0L); Error: UserArgumentMismatch 'names(shift)' (or 'names(start)') mismatch with 'levels(chromosome(x))' see ?"AlignedRead-class" In addition: Warning message: UserArgumentMismatch use 'shift'/'width' instead of 'start'/'end' -Abhi -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Pratap, Abhishek Sent: Wednesday, December 02, 2009 7:53 PM To: Patrick Aboyoun Cc: [email protected] Subject: Re: [Bioc-sig-seq] Plotting Coverage for inhouse genome Hi Patrick Thanks for letting me know how to search doc efficiently. Picking up on the coverage method, I tried the following. Also I would like to use only one chr, in this case (K-10_OM_revised.fasta *). How can I change the aln object to just one one specific chromosome. I tired few of my beginner tricks (aln$ K-10_OM_revised.fasta, aln[[K-10_OM_revised.fasta]] but dint work. I guess I am not using right method on aln object. cov_rLe <- coverage(x=aln, start=1, end=4832581, shift=0L, width=NULL,weight=1L,coords="leftmost",extend=0L); Error: UserArgumentMismatch 'names(shift)' (or 'names(start)') mismatch with 'levels(chromosome(x))' see ?"AlignedRead-class" In addition: Warning message: UserArgumentMismatch use 'shift'/'width' instead of 'start'/'end' Here 4832581 is the length of the genome. * Levels(chromosome(aln)) ======== Just to clear the confusion about the chromosome name. 175] "7:0:1" "7:1:0" "7:7:1" [178] "8:0:0" "K-10_OM_revised.fasta" "NM" [181] "QC" Cheers! -Abhi -----Original Message----- From: Patrick Aboyoun [mailto:[email protected]] Sent: Wednesday, December 02, 2009 6:19 PM To: Pratap, Abhishek Cc: Michael Lawrence; [email protected] Subject: Re: [Bioc-sig-seq] Plotting Coverage for inhouse genome Abhi, To answer your first question, there is a coverage method for AlignedRead objects in the ShortRead package. S4 methods can be hard to find in R's help pages, particularly if the methods for a generic are stored across multiple packages. When I'm unsure what is around, I use the showMethods function to get a list of available methods for an S4 generic: > suppressMessages(library(ShortRead)) > showMethods("coverage") Function: coverage (package IRanges) x="AlignedRead" x="AlignedXStringSet0" x="IRanges" x="MaskCollection" x="MaskedXString" x="MIndex" x="numeric" x="PairwiseAlignedFixedSubject" x="PairwiseAlignedFixedSubjectSummary" x="RangedData" x="RangesList" x="Views" From there I use a help command of the form help("<<generic>>,<<signature>>-method") > help("coverage,AlignedRead-method") In that man page you will find information on how to use coverage for an AlignedRead object. Once you have the coverage vectors (in the form of an RleList), you can use the approach Michael outlined for plotting. Patrick Michael Lawrence wrote: > On Wed, Dec 2, 2009 at 2:31 PM, Pratap, Abhishek > <[email protected]>wrote: > > >> Hi All >> >> After taking an exciting BioC course at FredHutch recently, I am trying >> to dive into BioC world to make more sense of NGS data. I would also >> like to thank the entire BioC team present there. You guys were simply >> great. I appreciate you all patiently answering tons of questions and >> taught some of the cool things we can do with BioC packages. >> >> For my current problem I would like to generate coverage plots for a >> small bacterial genome. I have the reads imported as a AlignedRead >> object and I am not sure how to proceed next. The help for the >> "coverage" method didn't get me very far. I am looking for some pointers >> to help me resolve the following questions. >> >> 1. How to create a RLE list from the AlignRead object using coverage >> method ? >> 2. Do I need to pack my reference genome as BSgenome data package in >> order to do this ? If yes I just have the sequence and no group II mask >> file. >> 3. Finally how to plot a RLE list. >> >> >> > This is a pretty difficult question to answer. Do you want to see all > chromosomes at once (like a karyotype plot)? An overview of entire > chromosomes? Or do you want to explore the data in an interactive genome > browser? > > There are many packages in Bioconductor for plotting this sort of data, > including GenomeGraphs and HilbertVis. For genome browsers, there's > rtracklayer and others. > > For example, with rtracklayer: > session <- browserSession() > session$coverage <- as(coverage, "RangedData") > > > > >> Thanks! >> -Abhi >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
