[BioC] subsetting transcriptDb

[Juliet Hannah]

All,

I am studying "Using the GenomicFeatures package" slides by Marc Carlson.

In the slides, a subset of the following corresponding to chr 9 is used.

library(GenomicFeatures)
mm9KG <- makeTranscriptDbFromUCSC(genome = "mm9", tablename = "knownGene")

How can I subset this transcriptDb object so that it contains only chr 9.

My goal is to use the statement

txExons <- exonsBy(mm9KGChr9)

where I believe mm9KGChr9 is what I am seeking above.

Apologies if I have missed something obvious.

Thanks,

Juliet


> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] BiocInstaller_1.2.1   GenomicFeatures_1.6.7 AnnotationDbi_1.16.11
[4] Biobase_2.14.0        GenomicRanges_1.6.6   IRanges_1.12.5

loaded via a namespace (and not attached):
 [1] biomaRt_2.10.0     Biostrings_2.22.0  BSgenome_1.22.0    DBI_0.2-5
 [5] RCurl_1.9-5        RSQLite_0.11.1     rtracklayer_1.14.4 tools_2.14.1
 [9] XML_3.9-4          zlibbioc_1.0.0