Hi Jesper, On 02/20/2014 02:13 PM, Jesper Gådin wrote:
Very true that it is quite difficult to find the documentation when one is not aware of its existence :P
Yeah, this has been a source of frustration for many people. And always a source of embarrassment (for us) when teaching our software to beginners. I've started to change this. In the upcoming version of BioC (2.14, scheduled for mid-April), when you'll do ?coverage, you'll get to choose between the 3 man pages that document coverage methods (there is one in IRanges, one in GenomicRanges, and one in GenomicAlignments). I want to generalize this to other generics that have methods spread across several packages (e.g. findOverlaps, the intra- and inter-range methods, etc...). Having to choose between several man pages every time you do e.g. ?findOverlaps is a minor annoyance compared to not being able to find the man page at all. (Note that if you already know where is your favorite man page, you'll be able to direct access it with e.g. ?GenomicRanges::findOverlaps). Nobody will ever need to use the insane ?`findOverlaps,GenomicRanges,GenomicRanges-method` to open that man page again. Ever! (it will still work though...) Cheers, H.
coverage() is fast and beautiful. Thanks! /Jesper On Wed, Feb 19, 2014 at 9:21 PM, Hervé Pagès <hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>> wrote: Hi Jesper, On 02/19/2014 08:44 AM, Michael Lawrence wrote: On Wed, Feb 19, 2014 at 8:39 AM, Jesper Gådin <jesper.ga...@gmail.com <mailto:jesper.ga...@gmail.com>>wrote: Hi Michael, Herves suggestion will probably work for my use case, but if there are any smoother ways it would be preferable. The use case is as follows: 1) calculate strand specific coverage over a region from GAlignments object (or file) At the moment I read a file using readGAlignmentsFromBam() with tag="XS", then filter it on "flag" and "mapq". Then I subset the resulting GAlignments in a minus and a plus -strand object. Then I calculate coverage by my own coverage function which uses the cigar information in the GAlignments object. This function is the one using cigarToRleList() at the moment. As I understand the coverage() function from the GenomicAlignments/IRanges package does not take into account cigars, or does it? It does take the coverage into account; specifically to exclude the introns from coverage. I think there's also an option to exclude deletions. Unfortunately the man page is not easy to access (you need to do ?`coverage,GAlignments-method`__), but it says: The methods for GAlignments and GAlignmentPairs objects do: coverage(grglist(x), ...) And if you do grglist() on a GAlignments or GAlignmentPairs objects, the ranges you get in the returned GRangesList object are calculated based on the CIGAR. Trust but verify. Here is how you can actually verify that coverage() does take the CIGAR into account: library(RNAseqData.HNRNPC.bam.__chr14) gal <- readGAlignments(RNAseqData.__HNRNPC.bam.chr14_BAMFILES[1]) cig_op_table <- cigarOpTable(cigar(gal)) First we pick up an alignment with an N in its CIGAR and do coverage() on it: > gal_with_N <- gal[which(cig_op_table[ , "N"] != 0)[1]] > gal_with_N GAlignments with 1 alignment and 0 metadata columns: seqnames strand cigar qwidth start end width <Rle> <Rle> <character> <integer> <integer> <integer> <integer> [1] chr14 + 55M2117N17M 72 19650072 19652260 2189 ngap <integer> [1] 1 --- seqlengths: chr1 chr10 ... chrY 249250621 135534747 ... 59373566 > coverage(gal_with_N)$chr14 integer-Rle of length 107349540 with 5 runs Lengths: 19650071 55 2117 17 87697280 Values : 0 1 0 1 0 Same thing with an alignment with an I in its CIGAR: > gal_with_I <- gal[which(cig_op_table[ , "I"] != 0)[1]] > gal_with_I GAlignments with 1 alignment and 0 metadata columns: seqnames strand cigar qwidth start end width <Rle> <Rle> <character> <integer> <integer> <integer> <integer> [1] chr14 - 64M1I7M 72 19411677 19411747 71 ngap <integer> [1] 0 --- seqlengths: chr1 chr10 ... chrY 249250621 135534747 ... 59373566 > coverage(gal_with_I)$chr14 integer-Rle of length 107349540 with 3 runs Lengths: 19411676 71 87937793 <tel:71%2087937793> Values : 0 1 0 Same thing with an alignment with a D in its CIGAR: > gal_with_D <- gal[which(cig_op_table[ , "D"] != 0)[1]] > gal_with_D GAlignments with 1 alignment and 0 metadata columns: seqnames strand cigar qwidth start end width <Rle> <Rle> <character> <integer> <integer> <integer> <integer> [1] chr14 + 38M1D34M 72 19659063 19659135 73 ngap <integer> [1] 0 --- seqlengths: chr1 chr10 ... chrY 249250621 135534747 ... 59373566 > coverage(gal_with_D)$chr14 integer-Rle of length 107349540 with 3 runs Lengths: 19659062 73 87690405 Values : 0 1 0 Seeing is believing, Cheers, H. I started to look at the applyPileups() in Rsamtools which I can get to calculate coverage using cigars, but not using the strand or flag information for filtering. That solution would start from a bam-file instead of a GAlignments object, and sure I can do the filtering outside R. But it would be very convenient to do it all from within R. If there are nice solutions starting from both a GAlignments and a bam-file it would be great! =) /Jesper On Tue, Feb 18, 2014 at 10:52 PM, Michael Lawrence < lawrence.mich...@gene.com <mailto:lawrence.mich...@gene.com>> wrote: Hi Jesper, Would you be willing to volunteer your use case? As Herve hinted, cigarToRleList and friends are low-level helpers. There may be an easier way to achieve what you want, or an opportunity to improve things. Michael On Mon, Feb 17, 2014 at 1:10 AM, Jesper Gådin <jesper.ga...@gmail.com <mailto:jesper.ga...@gmail.com>>wrote: Hi, Have come across a cigar-vector that is problematic to process. #load package library(GenomicAlignments) #load data (see attached file) load("2014-02-17-cigarExample.__rdata") #run function cigarToRleList cigarRle <- cigarToRleList(cigarExample) Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "IRanges") : integer overflow while summing elements in 'lengths' sessionInfo() R Under development (unstable) (2013-11-13 r64209) Platform: x86_64-unknown-linux-gnu (64-bit) 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicAlignments_0.99.18 Rsamtools_1.15.26 [3] Biostrings_2.31.12 XVector_0.3.6 [5] GenomicRanges_1.15.26 IRanges_1.21.23 [7] BiocGenerics_0.9.3 loaded via a namespace (and not attached): [1] BatchJobs_1.1-1135 BBmisc_1.5 BiocParallel_0.5.8 bitops_1.0-6 [5] brew_1.0-6 codetools_0.2-8 DBI_0.2-7 digest_0.6.4 [9] fail_1.2 foreach_1.4.1 iterators_1.0.6 plyr_1.8 [13] RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.0 tools_3.1.0 [17] zlibbioc_1.9.0 _________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel> [[alternative HTML version deleted]] _________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel> -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
