GenomicRanges BamFileList() not a function anymore?
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Sam McInturf ▴ 300
@sam-mcinturf-5291
Last seen 8.5 years ago
United States
Bioconductor users, I have been mapping my RNA seq reads using the GenomicRanges package, and was doing alright with it until I upgraded to R-3.0.0. At least I assume that the upgrade was the problem. After loading GenomicRanges the function BamFileList() is not longer a function. As below > library(GenomicRanges) Loading required package: BiocGenerics Loading required package: parallel Attaching package: âBiocGenericsâ The following objects are masked from âpackage:parallelâ: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from âpackage:statsâ: xtabs The following objects are masked from âpackage:baseâ: anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: IRanges > BamFileList() Error: could not find function "BamFileList" I work on two clusters, and both no longer work. What am I doing wrong, or what is an alternative to this method? I have been following the summerizeOverlaps vignette for mapping. thanks in advance! -- Sam McInturf [[alternative HTML version deleted]]
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@martin-morgan-1513
Last seen 6 weeks ago
United States
On 05/02/2013 01:35 PM, Sam McInturf wrote: > Bioconductor users, > I have been mapping my RNA seq reads using the GenomicRanges package, > and was doing alright with it until I upgraded to R-3.0.0. At least I > assume that the upgrade was the problem. After loading GenomicRanges the > function BamFileList() is not longer a function. As below > >> library(GenomicRanges) > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ?BiocGenerics? > > The following objects are masked from ?package:parallel?: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from ?package:stats?: > > xtabs > > The following objects are masked from ?package:base?: > > anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, > Filter, Find, get, intersect, lapply, Map, mapply, match, mget, > order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, > rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unlist > > Loading required package: IRanges > >> BamFileList() > Error: could not find function "BamFileList" > > I work on two clusters, and both no longer work. What am I doing wrong, or > what is an alternative to this method? I have been following the > summerizeOverlaps vignette for mapping. Hi Sam -- It's defined in the Rsamtools package, so library(Rsamtools) BamFileList() Martin > > thanks in advance! > > > > > _______________________________________________ > 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 > -- 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
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@james-w-macdonald-5106
Last seen 2 hours ago
United States
Hi Sam, On 5/2/2013 4:35 PM, Sam McInturf wrote: > Bioconductor users, > I have been mapping my RNA seq reads using the GenomicRanges package, > and was doing alright with it until I upgraded to R-3.0.0. At least I > assume that the upgrade was the problem. After loading GenomicRanges the > function BamFileList() is not longer a function. As below IIRC, the BamFileList function has never been in GenomicRanges, instead being defined in Rsamtools. Best, Jim > >> library(GenomicRanges) > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ?BiocGenerics? > > The following objects are masked from ?package:parallel?: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from ?package:stats?: > > xtabs > > The following objects are masked from ?package:base?: > > anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, > Filter, Find, get, intersect, lapply, Map, mapply, match, mget, > order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, > rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unlist > > Loading required package: IRanges > >> BamFileList() > Error: could not find function "BamFileList" > > I work on two clusters, and both no longer work. What am I doing wrong, or > what is an alternative to this method? I have been following the > summerizeOverlaps vignette for mapping. > > thanks in advance! > > > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Oh man, one day at a time i guess. Thanks for the help. On Thu, May 2, 2013 at 3:42 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Sam, > > > On 5/2/2013 4:35 PM, Sam McInturf wrote: > >> Bioconductor users, >> I have been mapping my RNA seq reads using the GenomicRanges package, >> and was doing alright with it until I upgraded to R-3.0.0. At least I >> assume that the upgrade was the problem. After loading GenomicRanges the >> function BamFileList() is not longer a function. As below >> > > IIRC, the BamFileList function has never been in GenomicRanges, instead > being defined in Rsamtools. > > Best, > > Jim > > > >> library(GenomicRanges) >>> >> Loading required package: BiocGenerics >> Loading required package: parallel >> >> Attaching package: āBiocGenericsā >> >> The following objects are masked from āpackage:parallelā: >> >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following object is masked from āpackage:statsā: >> >> xtabs >> >> The following objects are masked from āpackage:baseā: >> >> >> anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, >> Filter, Find, get, intersect, lapply, Map, mapply, match, mget, >> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, >> rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, >> tapply, union, unique, unlist >> >> Loading required package: IRanges >> >> BamFileList() >>> >> Error: could not find function "BamFileList" >> >> I work on two clusters, and both no longer work. What am I doing wrong, >> or >> what is an alternative to this method? I have been following the >> summerizeOverlaps vignette for mapping. >> >> thanks in advance! >> >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Sam McInturf [[alternative HTML version deleted]]
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