[BioC] Gviz

[Fiorella Schischlik [guest]]

Dear Bioconductor-community, 

I am using package Gviz to plot genomic regions.

library(Gviz)
biomTrack <- BiomartGeneRegionTrack(genome = "hg19", chromosome = chr, start = 63038367 , end = 64536346, name = "ENSEMBLE")

I would like to plot only those regions that are protein coding, so I tried this:

subTrack <-biomTrack[feature(biomTrack)=="protein_coding"]

When plotting the genomic region, I figured that eg. the gene with gene symbol PPM1H has 5 different transcripts with feature protein coding. When I searched for that gene in ensemble: http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000111110;r=12:63037762-63328817
only the first transcript has as biotype "Protein coding". The remaining transcripts are annotated as "Processed transcripts". 

My question: Is it possile to extract only those transcripts that are annotated as Protein coding in Ensemble? Is there a way to extract this information from the biomTrack object?

Thank you for any hint to solve my problem. 

Best regards, 
Fiorella







 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.16.0                     BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0                   
[4] Biostrings_2.28.0                  GenomicRanges_1.12.2               IRanges_1.18.1                    
[7] BiocGenerics_0.6.0                 Gviz_1.4.1                        

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.22.5   Biobase_2.20.0         biovizBase_1.8.0       bitops_1.0-5           cluster_1.14.4        
 [6] colorspace_1.2-2       DBI_0.2-7              dichromat_2.0-0        GenomicFeatures_1.12.1 Hmisc_3.10-1.1        
[11] labeling_0.1           lattice_0.20-15        munsell_0.4            plyr_1.8               RColorBrewer_1.0-5    
[16] RCurl_1.95-4.1         Rsamtools_1.12.3       RSQLite_0.11.3         rtracklayer_1.20.2     scales_0.2.3          
[21] stats4_3.0.0           stringr_0.6.2          tools_3.0.0            XML_3.96-1.1           zlibbioc_1.6.0     

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