Question: How Works The Subset Function For Biomartgeneregiontracks Of The Bioconductor Gviz Package?
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gravatar for andreas.dander
5.9 years ago by
andreas.dander10 wrote:

Hi,

can anybody help me with the BiomartGeneRegionTrack from the Gviz package of Bioconductor? My problem is the subset function. After creating a BiomartGeneRegionTrack for the chromosome 1 of hg19 from 179950000 to 180000000 this track contains 103 items.

In the following the code is depicted:

start <- 179950000;
end <- 180000000 
track <- BiomartGeneRegionTrack(genome = 'hg19', chromosome = 'chr1', start = start, end = end) 
length(track)

After creating a subset of this track from the same region there are only 51 items left.

subTrack <- subset(newTrack, from=start, to=end)
length(subTrack)

You can also plot these tracks with the command:

plotTracks(list(subTrack,newTrack), showId=TRUE)

Does anybody now how I can adjust this subset function that the result for this example are the same items then before subsetting?

Kind regards, Andreas

My sessionInfo() shows the following information:

R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale: 
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 
[3] LC_TIME=de_AT.UTF-8 LC_COLLATE=en_US.UTF-8 
[5] LC_MONETARY=de_AT.UTF-8 LC_MESSAGES=en_US.UTF-8 
[7] LC_PAPER=C LC_NAME=C 
[9] LC_ADDRESS=C LC_TELEPHONE=C 
[11] LC_MEASUREMENT=de_AT.UTF-8 LC_IDENTIFICATION=C 

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

other attached packages: 
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.0 
[2] org.Hs.eg.db_2.9.0 
[3] RSQLite_0.11.3 
[4] DBI_0.2-7 
[5] BSgenome.Hsapiens.UCSC.hg19_1.3.19 
[6] BSgenome_1.28.0 
[7] Biostrings_2.28.0 
[8] GenomicFeatures_1.12.1 
[9] AnnotationDbi_1.22.5 
[10] Biobase_2.20.0 
[11] GenomicRanges_1.12.2 
[12] IRanges_1.18.1 
[13] BiocGenerics_0.6.0 
[14] Gviz_1.4.1 

loaded via a namespace (and not attached): 
[1] biomaRt_2.16.0 biovizBase_1.8.0 bitops_1.0-5 cluster_1.14.4 
[5] colorspace_1.2-2 dichromat_2.0-0 Hmisc_3.10-1.1 labeling_0.1 
[9] lattice_0.20-15 munsell_0.4 plyr_1.8 RColorBrewer_1.0-5 
[13] RCurl_1.95-4.1 Rsamtools_1.12.3 rtracklayer_1.20.2 scales_0.2.3 
[17] stats4_3.0.1 stringr_0.6.2 tools_3.0.1 XML_3.96-1.1 
[21] zlibbioc_1.6.0
bioconductor • 1.9k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 5.9 years ago by andreas.dander10
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