## Display the list of genomes available at UCSC:
library(rtracklayer)
ucscGenomes()[ , "db"]
## Display the list of tables supported by makeTranscriptDbFromUCSC():
supportedUCSCtables()
## Not run:
# ## Retrieving a full transcript dataset for Yeast from UCSC:
# txdb1 <- makeTranscriptDbFromUCSC(genome="sacCer2", tablename="ensGene")
# ## End(Not run)
## Retrieving an incomplete transcript dataset for Mouse from UCSC
## (only transcripts linked to Entrez Gene ID 22290):
transcript_ids <- c(
"uc009uzf.1",
"uc009uzg.1",
"uc009uzh.1",
"uc009uzi.1",
"uc009uzj.1"
)
txdb2 <- makeTranscriptDbFromUCSC(genome="mm9", tablename="knownGene",
transcript_ids=transcript_ids)
txdb2
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