Question: Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
0
gravatar for Martin Rijlaarsdam
5.7 years ago by
Martin Rijlaarsdam190 wrote:
Hi, I am trying to use Gviz to retrieve info from specific regions on the genome using the BiomartGeneRegionTrack function. This goes fine with all chromosomes except X (and possibly Y, have not been able to test that). When I retrieve data for an empty region (20000-30000) all goes fine, but in a region with genes (17740000-17750000) the following error occurs: Error in FUN("X"[[1L]], ...) : Invalid chromosome identifier 'x' Please consider setting options(ucscChromosomeNames=FALSE) to allow for arbitrary chromosome identifiers. Setting options(ucscChromosomeNames=FALSE) as also described at https://stat.ethz.ch/pipermail/bioconductor/2013-April/052153.html completely breaks the code (nothing retrieved for any chromosome anymore). Moreover, I think I am using the correct identifier: "chrX" . Of interest, the ideogram and annotation track are generated fine with ' chromosome = "chrX" ' Thanks a lot for any help! Best, Martin Sample code: library(Gviz) #regions with genes st=17740000 ed=17750000 bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, chromosome="chrX", genome="hg19",showId = TRUE,background.title = "white", name="",fontsize=20,col="black") #empty area st=20000 ed=30000 bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, chromosome="chrX", genome="hg19",showId = TRUE,background.title = "white", name="",fontsize=20,col="black") itrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX",fontsize=20) gtrack <- GenomeAxisTrack(fontsize=20) st <- c(st) ed <- c(ed) strand <- c("*") gr <- c("ROI") annTrack <- AnnotationTrack(start=st, end=ed, strand=strand, chromosome="chrX", genome="hg19", feature="ROI", group=gr, id=paste("test"), name="generic annotation", stacking="squish", background.title = "white",col="black",fill="red",showFeatureId=TRUE,fontcolor="black") plotTracks(list(itrack,annTrack,gtrack,bmTrack),from=st, to=ed) ---- output of sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] Gviz_1.4.4 lumi_2.12.0 Biobase_2.20.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 AnnotationDbi_1.22.6 [5] beanplot_1.1 BiocInstaller_1.10.2 biomaRt_2.16.0 Biostrings_2.28.0 [9] biovizBase_1.8.1 bitops_1.0-5 BSgenome_1.28.0 cluster_1.14.4 [13] colorspace_1.2-2 DBI_0.2-7 dichromat_2.0-0 GenomicFeatures_1.12.2 [17] GenomicRanges_1.12.4 Hmisc_3.12-2 illuminaio_0.2.0 IRanges_1.18.2 [21] KernSmooth_2.23-10 labeling_0.2 lattice_0.20-15 limma_3.16.6 [25] MASS_7.3-27 Matrix_1.0-12 matrixStats_0.8.1 mclust_4.1 [29] methylumi_2.6.1 mgcv_1.7-24 minfi_1.6.0 multtest_2.16.0 [33] munsell_0.4.2 nleqslv_2.0 nlme_3.1-110 nor1mix_1.1-4 [37] plyr_1.8 preprocessCore_1.22.0 R.methodsS3_1.4.4 RColorBrewer_1.0-5 [41] RCurl_1.95-4.1 reshape_0.8.4 rpart_4.1-1 Rsamtools_1.12.3 [45] RSQLite_0.11.4 rtracklayer_1.20.4 scales_0.2.3 siggenes_1.34.0 [49] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 survival_2.37-4 [53] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.6.0 [[alternative HTML version deleted]]
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ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by Martin Rijlaarsdam190
Answer: Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
0
gravatar for Martin Rijlaarsdam
5.7 years ago by
Martin Rijlaarsdam190 wrote:
Hi, I am trying to use Gviz to retrieve info from specific regions on the genome using the BiomartGeneRegionTrack function. This goes fine with all chromosomes except X (and possibly Y, have not been able to test that). When I retrieve data for an empty region (20000-30000) all goes fine, but in a region with genes (17740000-17750000) the following error occurs: Error in FUN("X"[[1L]], ...) : Invalid chromosome identifier 'x' Please consider setting options(ucscChromosomeNames=FALSE) to allow for arbitrary chromosome identifiers. Setting options(ucscChromosomeNames=FALSE) as also described at https://stat.ethz.ch/pipermail/bioconductor/2013-April/052153.html completely breaks the code (nothing retrieved for any chromosome anymore). Moreover, I think I am using the correct identifier: "chrX" . Of interest, the ideogram and annotation track are generated fine with ' chromosome = "chrX" ' Thanks a lot for any help! Best, Martin Sample code: library(Gviz) #regions with genes st=17740000 ed=17750000 bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, chromosome="chrX", genome="hg19",showId = TRUE,background.title = "white", name="",fontsize=20,col="black") #empty area st=20000 ed=30000 bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, chromosome="chrX", genome="hg19",showId = TRUE,background.title = "white", name="",fontsize=20,col="black") itrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX",fontsize=20) gtrack <- GenomeAxisTrack(fontsize=20) st <- c(st) ed <- c(ed) strand <- c("*") gr <- c("ROI") annTrack <- AnnotationTrack(start=st, end=ed, strand=strand, chromosome="chrX", genome="hg19", feature="ROI", group=gr, id=paste("test"), name="generic annotation", stacking="squish", background.title = "white",col="black",fill="red",showFeatureId=TRUE,fontcolor="black") plotTracks(list(itrack,annTrack,gtrack,bmTrack),from=st, to=ed) ---- output of sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] Gviz_1.4.4 lumi_2.12.0 Biobase_2.20.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 AnnotationDbi_1.22.6 [5] beanplot_1.1 BiocInstaller_1.10.2 biomaRt_2.16.0 Biostrings_2.28.0 [9] biovizBase_1.8.1 bitops_1.0-5 BSgenome_1.28.0 cluster_1.14.4 [13] colorspace_1.2-2 DBI_0.2-7 dichromat_2.0-0 GenomicFeatures_1.12.2 [17] GenomicRanges_1.12.4 Hmisc_3.12-2 illuminaio_0.2.0 IRanges_1.18.2 [21] KernSmooth_2.23-10 labeling_0.2 lattice_0.20-15 limma_3.16.6 [25] MASS_7.3-27 Matrix_1.0-12 matrixStats_0.8.1 mclust_4.1 [29] methylumi_2.6.1 mgcv_1.7-24 minfi_1.6.0 multtest_2.16.0 [33] munsell_0.4.2 nleqslv_2.0 nlme_3.1-110 nor1mix_1.1-4 [37] plyr_1.8 preprocessCore_1.22.0 R.methodsS3_1.4.4 RColorBrewer_1.0-5 [41] RCurl_1.95-4.1 reshape_0.8.4 rpart_4.1-1 Rsamtools_1.12.3 [45] RSQLite_0.11.4 rtracklayer_1.20.4 scales_0.2.3 siggenes_1.34.0 [49] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 survival_2.37-4 [53] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.6.0
ADD COMMENTlink written 5.7 years ago by Martin Rijlaarsdam190
Dear Martin, You are trying to visualize data from two different sources which are using different chromosome names: * BiomartGeneRegionTrack based on e! which is using 1, 2, 3, ... X * IdeogramTrack based on UCSC which is using chr1, chr2, chr3, ... chrX You can combine both tracks together in the following way: library(Gviz) ## suppport non-UCSC chromosome names options(ucscChromosomeNames=FALSE) ##regions with genes st=17740000 ed=17750000 bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, chromosome="chrX", genome="hg19",showId = TRUE,background.title = "white", name="",fontsize=20,col="black") ## fix the seqlevels (e! is using 1,2, 3 ... X; UCSC is using chr1, chr2... chrX) library(GenomicRanges) ## we need function "seqlevels<-" seqlevels(ranges(bmTrack)) <- sprintf("chr%s", seqlevels(ranges(bmTrack))) ##empty area st=20000 ed=30000 bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, chromosome="chrX", genome="hg19",showId = TRUE,background.title = "white", name="",fontsize=20,col="black") ## fix the seqlevels (e! is using 1,2, 3 ... X; UCSC is using chr1, chr2... chrX) seqlevels(ranges(bmTrack)) <- sprintf("chr%s", seqlevels(ranges(bmTrack))) ## IdeogramTrack based on UCSC itrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX",fontsize=20) gtrack <- GenomeAxisTrack(fontsize=20) st <- c(st) ed <- c(ed) strand <- c("*") gr <- c("ROI") annTrack <- AnnotationTrack(start=st, end=ed, strand=strand, chromosome="chrX", genome="hg19", feature="ROI", group=gr, id=paste("test"), name="generic annotation", stacking="squish", background.title = "white",col="black",fill="red",showFeatureId=TRUE,fontcolor="black") plotTracks(list(itrack,annTrack,gtrack,bmTrack),from=st, to=ed) Best Robert On 16/07/13 14:06, Martin Rijlaarsdam wrote: > Hi, > > I am trying to use Gviz to retrieve info from specific regions on the > genome using the BiomartGeneRegionTrack function. This goes fine with > all chromosomes except X (and possibly Y, have not been able to test > that). When I retrieve data for an empty region (20000-30000) all goes > fine, but in a region with genes (17740000-17750000) the following > error occurs: > > Error in FUN("X"[[1L]], ...) : Invalid chromosome identifier 'x' > Please consider setting options(ucscChromosomeNames=FALSE) to allow > for arbitrary chromosome identifiers. > > Setting options(ucscChromosomeNames=FALSE) as also described at > https://stat.ethz.ch/pipermail/bioconductor/2013-April/052153.html > completely breaks the code (nothing retrieved for any chromosome > anymore). Moreover, I think I am using the correct identifier: "chrX" > . Of interest, the ideogram and annotation track are generated fine > with ' chromosome = "chrX" ' > > Thanks a lot for any help! > > Best, > Martin > > Sample code: > > library(Gviz) > #regions with genes > st=17740000 > ed=17750000 > bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, > chromosome="chrX", > genome="hg19",showId = TRUE,background.title = "white", > name="",fontsize=20,col="black") > #empty area > st=20000 > ed=30000 > bmTrack <- BiomartGeneRegionTrack(start=st, end=ed, > chromosome="chrX", > genome="hg19",showId = TRUE,background.title = "white", > name="",fontsize=20,col="black") > itrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX",fontsize=20) > gtrack <- GenomeAxisTrack(fontsize=20) > st <- c(st) > ed <- c(ed) > strand <- c("*") > gr <- c("ROI") > annTrack <- AnnotationTrack(start=st, end=ed, strand=strand, > chromosome="chrX", genome="hg19", feature="ROI", > group=gr, id=paste("test"), name="generic annotation", stacking="squish", > background.title = > "white",col="black",fill="red",showFeatureId=TRUE,fontcolor="black") > plotTracks(list(itrack,annTrack,gtrack,bmTrack),from=st, to=ed) > > ---- > > output of sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid parallel stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] Gviz_1.4.4 lumi_2.12.0 Biobase_2.20.0 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 > AnnotationDbi_1.22.6 > [5] beanplot_1.1 BiocInstaller_1.10.2 biomaRt_2.16.0 > Biostrings_2.28.0 > [9] biovizBase_1.8.1 bitops_1.0-5 BSgenome_1.28.0 > cluster_1.14.4 > [13] colorspace_1.2-2 DBI_0.2-7 dichromat_2.0-0 > GenomicFeatures_1.12.2 > [17] GenomicRanges_1.12.4 Hmisc_3.12-2 illuminaio_0.2.0 > IRanges_1.18.2 > [21] KernSmooth_2.23-10 labeling_0.2 lattice_0.20-15 > limma_3.16.6 > [25] MASS_7.3-27 Matrix_1.0-12 matrixStats_0.8.1 > mclust_4.1 > [29] methylumi_2.6.1 mgcv_1.7-24 minfi_1.6.0 > multtest_2.16.0 > [33] munsell_0.4.2 nleqslv_2.0 nlme_3.1-110 > nor1mix_1.1-4 > [37] plyr_1.8 preprocessCore_1.22.0 R.methodsS3_1.4.4 > RColorBrewer_1.0-5 > [41] RCurl_1.95-4.1 reshape_0.8.4 rpart_4.1-1 > Rsamtools_1.12.3 > [45] RSQLite_0.11.4 rtracklayer_1.20.4 scales_0.2.3 > siggenes_1.34.0 > [49] splines_3.0.1 stats4_3.0.1 stringr_0.6.2 > survival_2.37-4 > [53] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 > zlibbioc_1.6.0 > > _______________________________________________ > 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 >
ADD REPLYlink written 5.7 years ago by Robert Ivanek590
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