[BioC] Fwd: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack

[Martin Rijlaarsdam]

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