[BioC] RNA-seq pathway analysis in Canis familiaris

[Jessica Perry Hekman]

Hi, all. I am new to Bioconductor. I've tried hard to find the answer to 
my question in online documentation, so I apologize if I'm asking 
something which is already out there.

I'm hoping to perform RNA-seq pathway analysis using GAGE and Pahview. 
The RNAseq workflow documentation here:

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

shows that a known-genes annotation package is required for this 
workflow. The example uses human, TxDb.Hsapiens.UCSC.hg19.knownGene. 
Some other species have pre-built packages, but not dog.

I'm having trouble figuring out how to construct the equivalent package 
for Canis familiaris 3.1. This vignette

http://www.bioconductor.org/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf

(section 3) suggests that I can load a sqlite file based on UCSC known 
gene data. I can't quite figure out how to construct this sqlite file. 
Alternatively, I could load an annotation package such as 
TxDb.Hsapiens.UCSC.hg19.knownGene, and I'd be willing to build one of 
those for dog, but am not sure how.

Any advice or pointers to appropriate documentation would be hugely 
appreciated.

Thanks,
Jessica


-- 
Jessica P. Hekman, DVM, MS
PhD student, University of Illinois, Urbana-Champaign
Animal Sciences / Genetics, Genomics, and Bioinformatics