Hi Rubi, On 09/30/2013 07:33 AM, nimrod rubinstein wrote: > Hi Herv? and thanks for the response. > > I assume you meant 'gal[order(names(gal))]' rather than > 'gal[order(seqnames(gal))]' > in order to sort by QNAME (i.e. read ID)? My bad. You're right: seqnames is mapped to the RNAME field, not to the QNAME field. > > Using this, however, doesn't seem to sort gal by the same sorting rules > that sortBam or samtools sort -n does. Am I missing something? 2 reasons for that: (1) The result of 'order(names(gal))' depends on the collating sequence of the locale in use (see ?order and ?Comparison). So different users can get different results when doing 'gal[order(names(gal))]'. I don't know what collating sequence 'samtools sort -n' is using but even users using the same collating sequence might get different results, because of (2). (2) We don't know whether order() uses a "stable" sorting algorithm or not (AFAIK ?order doesn't tell). When a tie occurs (and when sorting by QNAME you can bet many ties will occur), a non- stable algo is free to break the tie in any way, whereas a stable algo is guaranteed to order the elements involved in the tie the same way they show up in the input. To summarize, 'gal[order(names(gal))]' and 'samtools sort -n' would be guaranteed to give the same result if both were using the same collating sequence and a stable sorting algo. I guess it's not the case. HTH, H. > > Thanks, > rubi > > > > On Mon, Sep 30, 2013 at 12:51 AM, Hervé Pagès <hpages at="" fhcrc.org=""> wrote: > >> Hi Rubi, >> >> 'gal[order(seqnames(gal))]' will sort GAlignments object 'gal' by QNAME. >> >> H. >> >> >> >> On 09/29/2013 12:32 PM, rubi [guest] wrote: >> >>> >>> Is there a way to sort the records in a GAlignments object by the QNAME, >>> as this object is created with the readGAlignmentsFromBam function where >>> the bam file and its corresponding index file must be sorted by RNAME and >>> POS. >>> >>> Unless I'm missing something the only way I see how can this be done is >>> read the bam into a data.table and sort that. >>> >>> -- output of sessionInfo(): >>> >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>> States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C >>> [5] LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] doParallel_1.0.3 iterators_1.0.6 foreach_1.4.1 >>> data.table_1.8.10 Rsamtools_1.13.44 Biostrings_2.29.19 >>> GenomicRanges_1.13.45 XVector_0.1.4 >>> [9] IRanges_1.19.38 BiocGenerics_0.7.5 >>> >>> loaded via a namespace (and not attached): >>> [1] bitops_1.0-6 codetools_0.2-8 stats4_3.0.2 tools_3.0.2 >>> zlibbioc_1.7.0 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >>> >> -- >> 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: hpages at fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319